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Merge pull request #88 from FAIRmat-NFDI/bring-in-examples
Bring in NOMAD examples
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| prune * | ||
| exclude * | ||
| recursive-include src/pynxtools_xps *.py *.json | ||
| include pyproject.toml README.md dev-requirements.txt | ||
| graft src/pynxtools_xps/nomad/examples |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| # | ||
| # Copyright The NOMAD Authors. | ||
| # | ||
| # This file is part of NOMAD. See https://nomad-lab.eu for further info. | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| # | ||
| """Entry points for XPS examples.""" | ||
|
|
||
| try: | ||
| from nomad.config.models.plugins import ExampleUploadEntryPoint | ||
| except ImportError as exc: | ||
| raise ImportError( | ||
| "Could not import nomad package. Please install the package 'nomad-lab'." | ||
| ) from exc | ||
|
|
||
| xps_example = ExampleUploadEntryPoint( | ||
| title="X-ray Photoelectron Spectroscopy (XPS)", | ||
| category="FAIRmat examples", | ||
| description=""" | ||
| This example presents the capabilities of the NOMAD platform to store and standardize X-ray Photoelectron Spectroscopy XPS data. | ||
| It shows the generation of a NeXus file according to the | ||
| [NXmpes](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes) | ||
| application definition from an example measurement file and a subseqeuent analysis of that data set. | ||
| """, | ||
| plugin_package="pynxtools_xps", | ||
| resources=["nomad/examples/*"], | ||
| ) |
137 changes: 137 additions & 0 deletions
137
src/pynxtools_xps/nomad/examples/E1 XPS data conversion to NeXus.ipynb
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| { | ||
| "cells": [ | ||
| { | ||
| "attachments": {}, | ||
| "cell_type": "markdown", | ||
| "id": "38f1916e-2d0f-4f81-9b00-fedc615a96aa", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# XPS conversion example\n", | ||
| "\n", | ||
| "In this notebook a XPS measurement file from a SPECS detector (using the native SPECS .sle format) is read and converted into the [NXmpes](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes) NeXus standard." | ||
| ] | ||
| }, | ||
| { | ||
| "attachments": {}, | ||
| "cell_type": "markdown", | ||
| "id": "dc099289-78f5-4357-b7d3-715dd20179da", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Create a NeXus file from measurement data\n", | ||
| "\n", | ||
| "To convert the available files to the NeXus format we use the convert function readily supplied by [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools)." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "7d2c1df4-1d96-4255-a18e-e323c69d32b4", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from pynxtools.dataconverter.convert import convert, logger\n", | ||
| "import logging\n", | ||
| "logger.setLevel(logging.ERROR)" | ||
| ] | ||
| }, | ||
| { | ||
| "attachments": {}, | ||
| "cell_type": "markdown", | ||
| "id": "bf441135-d4c5-4310-ae6e-39c87da1b726", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "The input parameters are defined as follows:\n", | ||
| "\n", | ||
| "**input_file**: The input files for the reader. This is a sle file from [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) (v.63), which is the propietary format of SPECS GmbH,and a YAML ELN file containing additional information not contained in the measurement file (e.g. user name).\n", | ||
| "\n", | ||
| "**reader**: The specific reader which gets called inside `pynxtools`. This is supplied in the [`pynxtools-xps`](https://github.com/FAIRmat-NFDI/pynxtools-xps) reader plugin. For XPS data, the reader is called `xps`.\n", | ||
| "\n", | ||
| "**nxdl**: The specific NXDL application definition to which the converted file should conform. For XPS this should be `NXmpes`, the subdefinition `NXxps`, or any further subdefinitions of the form `NXxps_<name>`.\n", | ||
| " \n", | ||
| "**output**: The output filename of the NeXus file." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "8e8a76ff-918e-483d-9ed1-5417613710e1", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "convert(\n", | ||
| " input_file=[\"EX439_S718_Au_in_25_mbar_O2.sle\", \"eln_data.yaml\"],\n", | ||
| " reader='xps',\n", | ||
| " nxdl='NXmpes',\n", | ||
| " remove_align=True,\n", | ||
| " output='Au_25_mbar_O2_no_align.nxs'\n", | ||
| ")" | ||
| ] | ||
| }, | ||
| { | ||
| "attachments": {}, | ||
| "cell_type": "markdown", | ||
| "id": "fa5fe119-0a72-4744-a84d-4d1258f55031", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## View the data with H5Web\n", | ||
| "\n", | ||
| "H5Web is a tool for visualizing any data in the h5 data format. Since the NeXus format builds opon h5 it can be used to view this data as well. We just import the package and call H5Web with the output filename from the convert command above.\n", | ||
| "\n", | ||
| "You can also view this data with the H5Viewer or other tools from your local filesystem." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "d4ff822a-4552-49b8-ba17-9b86fd8c2ac1", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from jupyterlab_h5web import H5Web" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "f62097ae-eb0f-4572-b8d9-bebc7266b43a", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "H5Web(\"Au_25_mbar_O2_no_align.nxs\")" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.10.10" | ||
| }, | ||
| "vscode": { | ||
| "interpreter": { | ||
| "hash": "0cbdf5d5ef28617c8bf3753ff15cd1b7b5539de5aaa68a35c3d38ca27e1ab0fa" | ||
| } | ||
| }, | ||
| "widgets": { | ||
| "application/vnd.jupyter.widget-state+json": { | ||
| "state": {}, | ||
| "version_major": 2, | ||
| "version_minor": 0 | ||
| } | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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