From 092537b4543278bf0b9ce8d181d1930660a06be8 Mon Sep 17 00:00:00 2001 From: Sherjeel Shabih Date: Fri, 7 Oct 2022 10:29:09 +0200 Subject: [PATCH] Better dependency management for dev, standalone, and a Nomad install (#50) * Added a pip-compile locked requirements for devs * Reverted nomad-lab install back * Fixed missing astroid version * cleanup + ease on dev reqs * Added a relaxed requirements.txt for installation with Nomad * Unrelaxed pyproject.toml dev reqs and reverted xarray to older version * Allowed python3.7 and fixed dask[array] version * Merge adapt-nexus-to-metainfo-changes and CI updates * cleanup * Brought in requirements.txt * draft refactoring and reorganizing of nomad-parser-nexus, decide first how tests should finally before structured, then the tests and absolute paths in the ipynbs and code sections should be changed * renaming tools; adding and fixing unit tests * fix some linting issues * addig reference data for testing nexus checker * fixing linting issues; adding test reference file * bringing Example to front * tested ipynb notebooks, added jupyterlab_h5web to the environment * improved descriptions, and placed jupyterlab in pyproject toml, tested compiling a dev-requirements locally successfully * updating readme.md as a result of testing * Added nexus definitions to the module package * fixing README files and the ipynb for APM * use dataconverter alias from command line * harmonising EM and MPES notebooks * Updated YAML file * Updated jupyter notebook for ellipsometry + DAT and YAML file * Delete ELLIPSOMETRY.NeXus.READER.EXAMPLE.02.ipynb * Delete test.yaml * fix data file locations Co-authored-by: Adam Fekete Co-authored-by: Adam Fekete Co-authored-by: kuehbachm Co-authored-by: sanbrock Co-authored-by: sanbrock <45483558+sanbrock@users.noreply.github.com> Co-authored-by: Carola Emminger Co-authored-by: cmmngr <98404894+cmmngr@users.noreply.github.com> --- .github/workflows/pylint.yml | 14 +- .gitignore | 197 + .gitmodules | 7 +- 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b/.github/workflows/pylint.yml index 44b9d1f9f..e988fbed4 100644 --- a/.github/workflows/pylint.yml +++ b/.github/workflows/pylint.yml @@ -16,21 +16,21 @@ jobs: git submodule sync --recursive git submodule update --init --recursive --jobs=4 python -m pip install --upgrade pip - pip install nomad-lab==1.1.3 --extra-index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - pip install astroid==2.5.1 - name: Install package run: | - python -m pip install . + python -m pip install --no-deps . + - name: Install dev requirements + run: | + python -m pip install -r dev-requirements.txt - name: pycodestyle run: | - python -m pycodestyle --ignore=E501,E701,E731 nexusparser tests --exclude=nexusparser/definitions + python -m pycodestyle --ignore=E501,E701,E731 nexusutils tests --exclude=nexusutils/definitions - name: pylint run: | - python -m pylint --load-plugins=pylint_mongoengine,nomad.metainfo.pylint_plugin nexusparser tests + python -m pylint nexusutils tests - name: mypy run: | - python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional --exclude='nexusparser/definitions/' tests + python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional nexusutils tests - name: Test with pytest if: ${{ always() }} run: | diff --git a/.gitignore b/.gitignore index 3e0aa677a..d15843202 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,204 @@ +# https://github.com/github/gitignore/blob/main/Global/macOS.gitignore +# General +.DS_Store +.AppleDouble +.LSOverride + +# Icon must end with two \r +Icon + + +# Thumbnails +._* + +# Files that might appear in the root of a volume +.DocumentRevisions-V100 +.fseventsd +.Spotlight-V100 +.TemporaryItems +.Trashes +.VolumeIcon.icns +.com.apple.timemachine.donotpresent + +# Directories potentially created on remote AFP share +.AppleDB +.AppleDesktop +Network Trash Folder +Temporary Items +.apdisk + +# https://github.com/github/gitignore/blob/main/Python.gitignore + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + + +# Custom settings + .mypy_cache/ .pyenv *.pyc *.txt +!requirements.txt +!dev-requirements.txt build/ nexusparser.egg-info/PKG-INFO .python-version diff --git a/.gitmodules b/.gitmodules index 4f013b42c..8c87edb2c 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,6 @@ -[submodule "nexusparser/definitions"] - path = nexusparser/definitions +[submodule "nexusutils/definitions"] + path = nexusutils/definitions + url = https://github.com/FAIRmat-Experimental/nexus_definitions.git +[submodule "nexusutils/nexus_definitions"] + path = nexusutils/definitions url = https://github.com/FAIRmat-Experimental/nexus_definitions.git diff --git a/.vscode/settings.json b/.vscode/settings.json index 3bae8ae7a..480310ae5 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -20,7 +20,7 @@ "python.linting.enabled": true, "python.linting.pylintArgs": [ "--load-plugins=nomad.metainfo.pylint_plugin", - "nexusparser", + "nexusutils", "tests" ], "python.testing.pytestArgs": [ diff --git a/DEVELOPER.md b/DEVELOPER.md deleted file mode 100644 index fdbc3d3ba..000000000 --- a/DEVELOPER.md +++ /dev/null @@ -1,209 +0,0 @@ -This is a NOMAD parser for [NEXUS](https://www.nexusformat.org/). It will read input in NEXUS format and output files and provide all information in NOMAD's unified Metainfo based Archive format. - -## Get started - -You should create a virtual environment. This is optional, but highly recommended as -the required nomad-lab pypi package requires many dependencies with specific versions -that might conflict with other libraries that you have installed. This was tested -with Python 3.7. - -If you don't have Python 3.7 installed on your computer, follow these commands: -``` -sudo add-apt-repository ppa:deadsnakes/ppa -sudo apt install python3.7 python3-dev libpython3.7-dev python-numpy - -``` - -You can now install your virtual environment with python3.7 interpreter - -``` -mkdir -cd -pip install virtualenv -virtualenv --python=python3.7 .pyenv -source .pyenv/bin/activate -``` - -Simply install our pypi package with pip: -``` -pip install --upgrade pip -pip install nomad-lab==1.1.1 --extra-index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple -``` - -Clone this project (or fork and then clone the fork). Go into the cloned directory and -directly run the parser from there: -``` -git clone https://github.com/nomad-coe/nomad-parser-nexus.git --branch master --recursive parser-nexus -cd parser-nexus -git submodule sync --recursive -git submodule update --init --recursive - -``` - -Install the remaining dev dependencies and install the package with: -``` -pip install -r requirements.txt -pip install -e .[all] -``` - -There are also a basic test framework written in [pytest](https://docs.pytest.org/en/stable/). -Run the test with: - -``` -pytest -sv tests -``` - -## Modules and their functions -### **Metainfo** - -First go to the nexus metainfo directory: -``` -cd nexusparser/metainfo -``` -This directory have several modules/files as following: - -| file | function| -|---|---| -|[generate.py](nexusparser/metainfo/generate.py)| This module contains functionality to generate metainfo source-code from metainfo definitions.| -|[templates/package.j2](nexusparser/metainfo/templates/package.j2)| A template to create/convert NEXUS classes with NOMAD schema.| -|[generate_nexus.py](nexusparser/metainfo/generate_nexus.py)|This module uses the `generate.py` module and the `package.j2` template to create classes in NOMAD format, with inheritance and extension of bases classes. It will create a `meta_nexus.py` file after running.| -|[meta_nexus.py](nexusparser/metainfo/meta_nexus.py)| This file is being created every time the generate_nexus.py script runs. It contains all base classes, application definitions, and contributed classes converted from NEXUS schema to NOMAD schema.| -|[test_nexus.py](nexusparser/metainfo/test_nexus.py)| After the meta_nexus.py file has been created, test_nexus.py can be run to test if it is correctly structured and working as desired.| -|[nexus.py](nexusparser/metainfo/nexus.py)| If the meta_nexus.py passes the above test, then run the following command to create/replace the current nexus.py file: ```cp meta_nexus.py nexus.py```. It is important that only, after testing meta_nexus.py and being sure that it is working appropriately, create nexus.py. Because nexus_py will be used by the actual parser later.| - -### **Tools** -This module contains several tools that are necessary to read user-specific experimental data and parse them into NOMAD. - -**1. Read nexus** - -First go to the nexus tools directory: -``` -cd nexusparser/tools -``` - -The module `nexus.py` reads HDF5 data file (i.e it is a user-specific data file, which contains numerical and metadata about the experiment. And it is formatted in NEXUS style.) - -*The environmental variable called "NEXUS_DEF_PATH" should be set to the directory, which contains application definitions as XML files. If this environmental variable is not defined, then code will first clone a directory from GitHub, which contains application definitions.* - -To set environmental variable, you can do: -``` -export 'NEXUS_DEF_PATH'= -``` - -***Testing nexus*** - -Following example dataset can be used to test `nexus.py` module `tests/data/nexus_test_data/201805_WSe2_arpes.nxs`. This is angular resolved photoelectron spectroscopy (ARPES) dataset and it is formatted according to the [NXarpes application definition of NEXUS](https://manual.nexusformat.org/classes/applications/NXarpes.html#nxarpes). Run the following command to test the `nexus.py` using example ARPES dataset: -``` -python test_parser.py -``` -*You should get "Testing of nexus.py is SUCCESSFUL." message, if everything goes as expected!* - - - -## Next steps - -Our documentation provides several resources that might be interesting: -- [How to write a parser](https://nomad-lab.eu/prod/rae/docs/parser.html). Provides - a more detailed tutorial on how to write a parser. -- [Introduction to the NOMAD Metainfo](https://nomad-lab.eu/prod/rae/docs/metainfo.html). - This explains how NOMAD data schema and can be extended and used within your parser. - -To get you parser included in NOMAD or ask further questions, you can: -- Use our forums at [matsci.org](https://matsci.org/c/nomad/32) -- Open an issue on the [nexus-parser GitHub project](https://github.com/nomad-coe/nomad-parser-nexus/issues) -- Write to [support@nomad-lab.eu](mailto:support@nomad-lab.eu) - -**Note!** The rest of this README.md is the usual text that applies to all NOMAD parsers. - - -This is a NOMAD parser for [EXAMPLE](https://www.nexus.eu/). It will read EXAMPLE input and -output files and provide all information in NOMAD's unified Metainfo based Archive format. - -## Preparing code input and output file for uploading to NOMAD - -NOMAD accepts `.zip` and `.tar.gz` archives as uploads. Each upload can contain arbitrary -files and directories. NOMAD will automatically try to choose the right parser for you files. -For each parser (i.e. for each supported code) there is one type of file that the respective -parser can recognize. We call these files `mainfiles` as they typically are the main -output file a code. For each `mainfile` that NOMAD discovers it will create an entry -in the database that users can search, view, and download. NOMAD will associate all files -in the same directory as files that also belong to that entry. Parsers -might also read information from these auxillary files. This way you can add more files -to an entry, even if the respective parser/code might not directly support it. - -For EXAMPLE please provide at least the files from this table if applicable to your -calculations (remember that you can provide more files if you want): - -|Input Filename| Description| -|--- | --- | -|`nexus.out` | **Mainfile** in EXAMPLE specific plain-text | - - -To create an upload with all calculations in a directory structure: - -``` -zip -r .zip /* -``` - -Go to the [NOMAD upload page](https://nomad-lab.eu/prod/rae/gui/uploads) to upload files -or find instructions about how to upload files from the command line. - -## Using the parser - -You can use NOMAD's parsers and normalizers locally on your computer. You need to install -NOMAD's pypi package: - -``` -pip install nomad-lab -``` - -To parse code input/output from the command line, you can use NOMAD's command line -interface (CLI) and print the processing results output to stdout: - -``` -nomad parse --show-archive -``` - -To parse a file in Python, you can program something like this: -```python -import sys -from nomad.cli.parse import parse, normalize_all - -# match and run the parser -archive = parse(sys.argv[1]) -# run all normalizers -normalize_all(archive) - -# get the 'main section' section_run as a metainfo object -section_run = archive.section_run[0] - -# get the same data as JSON serializable Python dict -python_dict = section_run.m_to_dict() -``` - -## Developing the parser - -Create a virtual environment to install the parser in development mode: - -``` -pip install virtualenv -virtualenv -p `which python3` .pyenv -source .pyenv/bin/activate -``` - -Install NOMAD's pypi package: - -``` -pip install nomad-lab -``` - -Clone the parser project and install it in development mode: - -``` -git clone https://github.com/nomad-coe/nomad-parser-nexus.git parser-nexus -pip install -e parser-nexus -``` - -Running the parser now, will use the parser's Python code from the clone project. - -$parserSpecific$ diff --git a/LICENSE.txt b/LICENSE similarity index 100% rename from LICENSE.txt rename to LICENSE diff --git a/MANIFEST.in b/MANIFEST.in index 6deec5eb5..126d8db70 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,4 +1,4 @@ -recursive-include nexusparser/definitions/base_classes/ *.xml -recursive-include nexusparser/definitions/applications/ *.xml -recursive-include nexusparser/definitions/contributed_definitions/ *.xml -include nexusparser/definitions/ *.xsd +recursive-include nexusutils/definitions/base_classes/ *.xml +recursive-include nexusutils/definitions/applications/ *.xml +recursive-include nexusutils/definitions/contributed_definitions/ *.xml +include nexusutils/definitions/ *.xsd diff --git a/README.md b/README.md index 12ac62265..41fc0ab33 100644 --- a/README.md +++ b/README.md @@ -1,22 +1,104 @@ -This is a NOMAD parser for [NEXUS](https://www.nexusformat.org/). It will read input in NEXUS format and output files and provide all information in NOMAD's unified Metainfo based Archive format. +This is a software for developing ontologies and instances of ontologies with +[NeXus](https://www.nexusformat.org/). The software serves two aims. + +First, it offers users a tool with which they can +create specific data files packaging together numerical data and metadata from +experiments which can originate from technology partners and/or text file output +from an electronic lab notebook (ELN). + +Second, the software is used in the German National Research Data Infrastructure +(German NFDI) project FAIRmat, here specifically in the NOMAD OASIS research data +management (RDM) system, to serve as a set of parsers which enable users of a NOMAD +Oasis instance to create data and metadata entries from experiments so that NOMAD Oasis +understands the specific logic and terminology of the scientific field. + +The software tools are located inside the module subdirectory 'nexusutils'and they are +shipped with unit tests located in the subdirectory 'tests'. +Some examples with real datasets are also provided in the subdirectory 'examples' +in which Jupyter Notebooks are guiding through the process of converting instrument raw +data into the NeXus standard and then aloow the visualisation of the hierarchical contents +of the generated NeXus file in JupyterLab. ## Getting started +You should create a virtual environment. We tested on Ubuntu with Python 3.7. -Install the nexusparser as a standalone tool: +If you don't have Python 3.7 installed on your computer, follow these commands: +``` +sudo add-apt-repository ppa:deadsnakes/ppa +sudo apt install python3.7 python3-dev libpython3.7-dev python-numpy + +``` + +You can now install your virtual environment with a python3.7 interpreter + +``` +mkdir +cd +pip install virtualenv +virtualenv --python=python3.7 .pyenv +source .pyenv/bin/activate +pip install pip-tools ``` -pip install nexusparser --extra-index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple + +This software can be used independently of a NOMAD or NOMAD Oasis instance. +Clone this project (or fork and then clone the fork). +Go into the cloned directory and directly run the parser from there: + +Now you have to decide your role. Are you a user or a developer? + +### I want to use nexusutils as a user +If you are a user you should install nexusutils as a standalone tool: +``` +pip install nexusutils --extra-index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple ``` -This project also includes standalone tools that can be used without installing Nomad. +### I am a developer and want to explore or contribute -***If you want to use it as a Nomad parser, see [below](#using-the-project-as-a-parser-in-nomad).*** +Install package with its dependencies: -## YAML2NXDL +``` +git clone https://github.com/nomad-coe/nomad-parser-nexus.git --branch master --recursive nexusutils +cd nexusutils +git submodule sync --recursive +git submodule update --init --recursive --jobs=4 +python -m pip install --upgrade pip +python -m pip install -e . +python -m pip install -e .[dev] +``` + +To be able to run jupyerlab with the NeXus file viewer H5Web, you also need the foolwing packages + +``` +python -m pip install jupyterlab +python -m pip install jupyterlab_h5web[full]==6.0.1 +``` + +## Test this software +Especially relevant for developers, there exists a basic test framework written in +[pytest](https://docs.pytest.org/en/stable/) which can be used as follows: + +``` +python -m pytest -sv tests +``` + +## Individual modules of this software and their functions + +### **nyaml2nxdl** +This module is a tool which automatically converts YAML files containing specifications for NeXus +base classes and/or application definitions, i.e. data schemes, into specifically formatted XML files +that follow the conventions used in NeXus. The tool works in two directions: Either a YAML file can +be converted to a NXDL XML file or a NXDL XML file can be converted into a YAML. +NXDL XML files have an own XML and XSD rule set that was developed and is maintained +by the NeXus International Advisory Committee (NIAC). The nyaml2nxdl converter implements this rule set. + +The main purpose of the tool is to support developers with a simplified +editing and writing experience when they wish to explore, modified, i.e. work with +NeXus base classes and application definitions. ```console -user@box:~$ python -m nexusparser.tools.yaml2nxdl.yaml2nxdl +user@box:~$ nyaml2nxdl --help -Usage: python yaml2nxdl.py [OPTIONS] +Usage: nyaml2nxdl.py [OPTIONS] Options: --input-file TEXT The path to the input data file to read. @@ -24,17 +106,39 @@ Options: write the base class name with no extension. --verbose Addictional std output info is printed to help debugging. --help Show this message and exit. - ``` -Further documentation: [README.md](nexusparser/tools/yaml2nxdl/README.md) +Further documentation: [README.md](nyaml2nxdl/README.md) + -## Dataconverter +### **dataconverter** +This module is a tool which enables users to create instances of NeXus/HDF5 files. +The instances are specific for the experiment and technique. +Each instance supports a combination of specifically-versioned software components: +A NeXus application definition, an associated referred to set of base classes, +and an experiment/technique-specific dataconverter (aka parser). -Converts experimental data to Nexus/HDF5 files based on any provided NXDL. +The main purpose of these parsers is to create an instance of a NeXus/HDF5 file that is +formatted in accordance with the respective NeXus application definition. +This means the parser eventually transcodes and copies data and metadata within specifically +formatted file and representations, like ELNs, of a scientific community and/or +technology partner. + +The dataconverter implements a concept of a generic parser, which internally calls +the above-mentioned experimental-method-specific parser. +Currently, the generic parser maintains one dictionary object in which all +data and metadata to be written are collected and exported to HDF5 afterwards. +The role of the generic parser is to resolve the structure of the NeXus application +definition and decorate the HDF5 files with attributes, fields, and groups +as it is required by NeXus, so that the dataconverter can yield a properly +formatted NeXus/HDF5 file. + +The role of the specific parsers is to fill this dictionary. Parsers are separated +to avoid that a single parser becomes too complex in its implementation. ```console -user@box:~$ python -m nexusparser.tools.dataconverter.convert --help +user@box:~$ dataconverter --help + Usage: convert.py [OPTIONS] Options: @@ -43,49 +147,50 @@ Options: --reader TEXT The reader to use. --nxdl TEXT The name of the NXDL file to use without extension. [required] - --output TEXT The path to the output Nexus file to be generated. + --output TEXT The path to the output NeXus file to be generated. --generate-template Just print out the template generated from given NXDL file. --help Show this message and exit. ``` -Further documentation: [README.md](nexusparser/tools/dataconverter/README.md) +Further documentation: [README.md](dataconverter/README.md) -## Nexus Checker +Inspect also specific README.md of the respective parser(s) you wish to use +or contribute to so that you can learn how these parser(s) work, which input data +they expect, and what which output they yield. -Outputs a debug log for a given Nexus file. +### **read_nexus** +This utility outputs a debug log for a given NeXus file by annotating the data and +metadata entries with the schema definitions from the respective base classes and +application definitions the file content is referring to. ```console -user@box:~$ python -m nexusparser.tools.nexus +user@box:~$ read_nexus ``` +*The environmental variable called "NEXUS_DEF_PATH" can be set to +a directory, which contains the NeXus definitions as XML files. If this environmental +variable is not defined, the module will use the dinfitions in its bundle.* -# Using the project as a parser in Nomad -You should create a virtual environment. This is optional, but highly recommended as -the required nomad-lab pypi package requires many dependencies with specific versions -that might conflict with other libraries that you have installed. This was tested -with Python 3.7. - -If you don't have Python 3.7 installed on your computer, follow these commands: +An environmental variable can be set as follows: ``` -sudo add-apt-repository ppa:deadsnakes/ppa -sudo apt install python3.7 python3-dev libpython3.7-dev python-numpy - -``` - -You can now install your virtual environment with python3.7 interpreter - -``` -mkdir -cd -pip install virtualenv -virtualenv --python=python3.7 .pyenv -source .pyenv/bin/activate +export 'NEXUS_DEF_PATH'= ``` -Simply install the nexusparser pypi package with all dependencies: -``` -pip install --upgrade pip -pip install nexusparser[nomad] --extra-index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple -``` \ No newline at end of file +## Next steps + +Our documentation provides several resources that might be interesting for developers of NOMAD (Oasis): +- [How to write a parser](https://nomad-lab.eu/prod/rae/docs/parser.html). + Provides a more detailed tutorial on how to write a parser for NOMAD. +- [Introduction to the NOMAD Metainfo](https://nomad-lab.eu/prod/rae/docs/metainfo.html). + This explains how the NOMAD data schema, the so-called NOMAD MetaInfo, can be extended + and used within your parser. A contextualization of the NOMAD MetaInfo is available + in the scientific literature https://doi.org/10.1038/s41524-017-0048-5. + +## Questions, suggestions? +To ask further questions, to make suggestions how we can improve these tools, to +get advice on how to build on this work, or to get your parser included into NOMAD, you can: +- Open an issue on the [nexus-parser GitHub project](https://github.com/nomad-coe/nomad-parser-nexus/issues) +- Use our forums at [matsci.org](https://matsci.org/c/nomad/32) +- Write to [support@nomad-lab.eu](mailto:support@nomad-lab.eu) diff --git a/dev-requirements.txt b/dev-requirements.txt new file mode 100644 index 000000000..5031cd274 --- /dev/null +++ b/dev-requirements.txt @@ -0,0 +1,446 @@ +# +# This file is autogenerated by pip-compile with python 3.7 +# To update, run: +# +# pip-compile --extra=dev --output-file=dev-requirements.txt pyproject.toml +# +anyio==3.6.1 + # via jupyter-server +argon2-cffi==21.3.0 + # via jupyter-server +argon2-cffi-bindings==21.2.0 + # via argon2-cffi +asciitree==0.3.3 + # via zarr +ase==3.22.1 + # via nexusutils (pyproject.toml) +astroid==2.12.10 + # via + # nexusutils (pyproject.toml) + # pylint +attrs==22.1.0 + # via + # jsonschema + # pytest +backcall==0.2.0 + # via ipython +beautifulsoup4==4.11.1 + # via nbconvert +bleach==5.0.1 + # via nbconvert +certifi==2022.9.24 + # via requests +cffi==1.15.1 + # via argon2-cffi-bindings +charset-normalizer==2.1.1 + # via requests +click==8.1.3 + # via nexusutils (pyproject.toml) +cloudpickle==2.2.0 + # via dask +coverage[toml]==6.5.0 + # via pytest-cov +cycler==0.11.0 + # via matplotlib +dask[array]==2022.2.0 + # via hyperspy +debugpy==1.6.3 + # via ipykernel +decorator==5.1.1 + # via + # ipyparallel + # ipython +defusedxml==0.7.1 + # via nbconvert +dill==0.3.5.1 + # via + # hyperspy + # pylint +entrypoints==0.4 + # via + # ipyparallel + # jupyter-client + # numcodecs +fasteners==0.18 + # via zarr +fastjsonschema==2.16.2 + # via nbformat +flatdict==4.0.1 + # via nexusutils (pyproject.toml) +fonttools==4.37.4 + # via matplotlib +fsspec==2022.8.2 + # via + # dask + # hyperspy +h5grove==1.1.0 + # via jupyterlab-h5web +h5py==3.7.0 + # via + # h5grove + # hyperspy + # nexusutils (pyproject.toml) +hyperspy==1.7.2 + # via nexusutils (pyproject.toml) +idna==3.4 + # via + # anyio + # requests +imageio==2.22.1 + # via + # hyperspy + # scikit-image +importlib-metadata==5.0.0 + # via + # click + # hyperspy + # jsonschema + # nbconvert + # nbformat + # numba + # pint + # pluggy + # prettytable + # pytest + # xarray +importlib-resources==5.9.0 + # via jsonschema +iniconfig==1.1.1 + # via pytest +ipykernel==6.16.0 + # via ipyparallel +ipyparallel==8.4.1 + # via hyperspy +ipython==7.34.0 + # via + # hyperspy + # ipykernel + # ipyparallel +isort==5.10.1 + # via pylint +jedi==0.18.1 + # via ipython +jinja2==3.1.2 + # via + # hyperspy + # jupyter-server + # nbconvert +jsonschema==4.16.0 + # via nbformat +jupyter-client==7.3.5 + # via + # ipykernel + # ipyparallel + # jupyter-server + # nbclient +jupyter-core==4.11.1 + # via + # jupyter-client + # jupyter-server + # nbconvert + # nbformat +jupyter-server==1.19.1 + # via jupyterlab-h5web +jupyterlab-h5web==6.0.1 + # via nexusutils (pyproject.toml) +jupyterlab-pygments==0.2.2 + # via nbconvert +kiwisolver==1.4.4 + # via matplotlib +lazy-object-proxy==1.7.1 + # via astroid +llvmlite==0.39.1 + # via numba +locket==1.0.0 + # via partd +markupsafe==2.1.1 + # via + # jinja2 + # nbconvert +matplotlib==3.5.3 + # via + # ase + # hyperspy +matplotlib-inline==0.1.6 + # via + # ipykernel + # ipython +mccabe==0.7.0 + # via pylint +mistune==2.0.4 + # via nbconvert +mpmath==1.2.1 + # via sympy +mypy==0.982 + # via nexusutils (pyproject.toml) +mypy-extensions==0.4.3 + # via mypy +natsort==8.2.0 + # via hyperspy +nbclient==0.6.8 + # via nbconvert +nbconvert==7.1.0 + # via jupyter-server +nbformat==5.6.1 + # via + # jupyter-server + # nbclient + # nbconvert +nest-asyncio==1.5.6 + # via + # ipykernel + # jupyter-client + # nbclient +networkx==2.6.3 + # via scikit-image +numba==0.56.2 + # via + # hyperspy + # sparse +numcodecs==0.10.2 + # via zarr +numexpr==2.8.3 + # via hyperspy +numpy==1.21.6 + # via + # ase + # dask + # h5grove + # h5py + # hyperspy + # imageio + # matplotlib + # nexusutils (pyproject.toml) + # numba + # numcodecs + # numexpr + # pandas + # pywavelets + # scikit-image + # scipy + # sparse + # tifffile + # xarray + # zarr +orjson==3.8.0 + # via h5grove +packaging==21.3 + # via + # dask + # hyperspy + # ipykernel + # jupyter-server + # matplotlib + # nbconvert + # numexpr + # pint + # pytest + # scikit-image +pandas==1.3.5 + # via + # nexusutils (pyproject.toml) + # xarray +pandocfilters==1.5.0 + # via nbconvert +parso==0.8.3 + # via jedi +partd==1.3.0 + # via dask +pexpect==4.8.0 + # via ipython +pickleshare==0.7.5 + # via ipython +pillow==9.2.0 + # via + # imageio + # matplotlib + # scikit-image +pint==0.18 + # via hyperspy +pkgutil-resolve-name==1.3.10 + # via jsonschema +platformdirs==2.5.2 + # via pylint +pluggy==1.0.0 + # via pytest +prettytable==3.4.1 + # via hyperspy +prometheus-client==0.14.1 + # via jupyter-server +prompt-toolkit==3.0.31 + # via ipython +psutil==5.9.2 + # via + # ipykernel + # ipyparallel +ptyprocess==0.7.0 + # via + # pexpect + # terminado +py==1.11.0 + # via pytest +pycodestyle==2.9.1 + # via nexusutils (pyproject.toml) +pycparser==2.21 + # via cffi +pygments==2.13.0 + # via + # ipython + # nbconvert +pylint==2.15.3 + # via nexusutils (pyproject.toml) +pyparsing==3.0.9 + # via + # matplotlib + # packaging +pyrsistent==0.18.1 + # via jsonschema +pytest==7.1.3 + # via + # nexusutils (pyproject.toml) + # pytest-cov + # pytest-timeout +pytest-cov==4.0.0 + # via nexusutils (pyproject.toml) +pytest-timeout==2.1.0 + # via nexusutils (pyproject.toml) +python-dateutil==2.8.2 + # via + # hyperspy + # ipyparallel + # jupyter-client + # matplotlib + # pandas +pytz==2022.4 + # via pandas +pywavelets==1.3.0 + # via scikit-image +pyyaml==6.0 + # via + # dask + # hyperspy + # nexusutils (pyproject.toml) +pyzmq==24.0.1 + # via + # ipykernel + # ipyparallel + # jupyter-client + # jupyter-server +requests==2.28.1 + # via hyperspy +scikit-image==0.19.3 + # via hyperspy +scipy==1.7.3 + # via + # ase + # hyperspy + # scikit-image + # sparse +send2trash==1.8.0 + # via jupyter-server +six==1.16.0 + # via + # bleach + # python-dateutil +sniffio==1.3.0 + # via anyio +soupsieve==2.3.2.post1 + # via beautifulsoup4 +sparse==0.13.0 + # via hyperspy +structlog==22.1.0 + # via nexusutils (pyproject.toml) +sympy==1.10.1 + # via hyperspy +terminado==0.16.0 + # via jupyter-server +tifffile==2021.11.2 + # via + # h5grove + # hyperspy + # scikit-image +tinycss2==1.1.1 + # via nbconvert +tomli==2.0.1 + # via + # coverage + # mypy + # pylint + # pytest +tomlkit==0.11.5 + # via pylint +toolz==0.12.0 + # via + # dask + # hyperspy + # partd +tornado==6.2 + # via + # ipykernel + # ipyparallel + # jupyter-client + # jupyter-server + # terminado +tqdm==4.64.1 + # via + # hyperspy + # ipyparallel +traitlets==5.4.0 + # via + # ipykernel + # ipyparallel + # ipython + # jupyter-client + # jupyter-core + # jupyter-server + # matplotlib-inline + # nbclient + # nbconvert + # nbformat +traits==6.4.1 + # via hyperspy +typed-ast==1.5.4 + # via + # astroid + # mypy + # nexusutils (pyproject.toml) +types-pyyaml==6.0.12 + # via nexusutils (pyproject.toml) +typing-extensions==4.3.0 + # via + # anyio + # argon2-cffi + # astroid + # importlib-metadata + # jsonschema + # kiwisolver + # mypy + # numcodecs + # pylint + # structlog + # xarray +urllib3==1.26.12 + # via requests +wcwidth==0.2.5 + # via + # prettytable + # prompt-toolkit +webencodings==0.5.1 + # via + # bleach + # tinycss2 +websocket-client==1.4.1 + # via jupyter-server +wrapt==1.14.1 + # via astroid +xarray==0.20.2 + # via nexusutils (pyproject.toml) +zarr==2.12.0 + # via hyperspy +zipp==3.8.1 + # via + # importlib-metadata + # importlib-resources + +# The following packages are considered to be unsafe in a requirements file: +# setuptools diff --git a/tests/data/tools/dataconverter/readers/apm/README.md b/examples/README.md similarity index 50% rename from tests/data/tools/dataconverter/readers/apm/README.md rename to examples/README.md index 220777f58..0e59629cd 100644 --- a/tests/data/tools/dataconverter/readers/apm/README.md +++ b/examples/README.md @@ -1,38 +1,14 @@ -The tools of the NOMAD parser for [NEXUS](https://www.nexusformat.org/) can also be used -without a NOMAD OASIS installation. There are two main use cases: -- Use the DATACONVERTER/apm for transcoding vendor and community files to +The tools can be used with the following two main use cases: +- Use the DATACONVERTER/apm for transcoding vendor and community files to NeXus files so that these are compliant with a specific NeXus application definition [NEXUS-FAIRMAT-PROPOSAL](https://fairmat-experimental.github.io/nexus-fairmat-proposal/). In this example NXapm. -- Use the YAML2NXDL converter during editing and developing +- Use the NYAML2NXDL converter during editing and developing NeXus base classes and application definitions. ## Getting started - prepare your environment -It is recommended to install the tool in an own virtual environment as -some installation steps will install specific versions of packages which -might be in conflict with existent ones in your environment. -You can install the tools as standalone tools. We make the following assumptions: -- You have python in version 3.7 installed. Higher versions can be used but might - need modifications for specific packages on which nomad-parser-nexus depends. -- You can but do not need to be inside a conda environment. - -``` -pip install virtualenv && virtualenv --python=python3.7 .nexusenv && source .nexusenv/bin/activate -pip install --upgrade pip==22.2.2 && pip install --upgrade nodejs==0.1.1 -pip install jupyterlab_h5web[full]==6.0.1 -``` - -## Getting started - install the nomad-parser-nexus tool - -``` -git clone https://github.com/nomad-coe/nomad-parser-nexus.git --recursive -cd nomad-parser-nexus/ -git branch -a -pip install -e . -``` - -With these two steps the installation is complete. +Please follow the **installation guide for developers** in the main README ### Using the tool @@ -68,13 +44,3 @@ cleaner for the chrome browser than for firefox. There is a jupyter notebook (ipynb) for each technique which you should use to interact with the tool. - -## Where should one place the files -For the dataconverter, you can find the respective notebooks in - -``` -tests/data/tools/dataconverter/readers/apm/ -``` - -Go one directory deeper to explore the specific jupyter notebook for your method of choice. - diff --git a/examples/apm/Apm.NeXus.Apm.Example.1.ipynb b/examples/apm/Apm.NeXus.Apm.Example.1.ipynb new file mode 100644 index 000000000..66ff27335 --- /dev/null +++ b/examples/apm/Apm.NeXus.Apm.Example.1.ipynb @@ -0,0 +1,844 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## NOMAD-PARSER-NEXUS/DATACONVERTER demo for Atom Probe Microscopy (APM) data" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 1:** Check that everything is ready to go and download example data for APM. " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "check the result of the query below if the modules `jupyterlab_h5web` and `nexusutils` are installed in your environement. Note that next to the name nexusutils you should see the directory in which it is installed. Otherwise make sure that you followed the instructions in the `README` files: \n", + "- how to set up a development environment as in the main README \n", + "- lauch the jupyter lab from this environement as in the README of folder `examples`" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "h5py 3.7.0\n", + "jupyter_client 7.3.5\n", + "jupyter-core 4.11.1\n", + "jupyter-server 1.19.1\n", + "jupyterlab-h5web 6.0.1\n", + "jupyterlab-pygments 0.2.2\n", + "nexusutils 0.0.1\n", + "config dir: /home/mkuehbach/.jupyter\n", + " jupyterlab_h5web \u001b[32m enabled \u001b[0m\n", + " - Validating...\n", + " jupyterlab_h5web 5.0.0 \u001b[32mOK\u001b[0m\n", + " jupyter_nbextensions_configurator \u001b[32m enabled \u001b[0m\n", + " - Validating...\n", + " jupyter_nbextensions_configurator 0.4.1 \u001b[32mOK\u001b[0m\n", + "config dir: /home/mkuehbach/.local/etc/jupyter\n", + " jupyterlab \u001b[32m enabled \u001b[0m\n", + " - Validating...\n", + " jupyterlab 3.4.3 \u001b[32mOK\u001b[0m\n", + " jupyterlab_h5web \u001b[32m enabled \u001b[0m\n", + " - Validating...\n", + " jupyterlab_h5web 5.0.0 \u001b[32mOK\u001b[0m\n", + "JupyterLab v3.4.3\n", + "/home/mkuehbach/.local/share/jupyter/labextensions\n", + " jupyterlab_pygments v0.2.2 \u001b[32menabled\u001b[0m \u001b[32mOK\u001b[0m (python, jupyterlab_pygments)\n", + " jupyterlab-h5web v5.0.0 \u001b[32menabled\u001b[0m \u001b[32mOK\u001b[0m (python, jupyterlab_h5web)\n", + " @jupyter-widgets/jupyterlab-manager v3.1.0 \u001b[32menabled\u001b[0m \u001b[32mOK\u001b[0m (python, jupyterlab_widgets)\n", + "\n", + "Python 3.7.14\n" + ] + } + ], + "source": [ + "! pip list | grep 'h5py\\|nexus\\|jupyter' && jupyter serverextension list && jupyter labextension list && python -V" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Set the nexusutils directory." + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Current working directory\n", + "/home/mkuehbach/SPRINT-9/20221006_refactor_nomad_parser_nexus/nomad-parser-nexus/examples/apm\n", + "Base/home/root directory of the nomad-parser-nexus\n", + "/home/mkuehbach/SPRINT-9/20221006_refactor_nomad_parser_nexus/nomad-parser-nexus\n" + ] + } + ], + "source": [ + "import os\n", + "print('Current working directory')\n", + "print(os.getcwd())\n", + "nexus_dir = os.getcwd().replace('/examples/apm', '')\n", + "# import nexusutils\n", + "# nexus_dir = os.path.dirname(nexusutils.__file__)\n", + "print('Base/home/root directory of the nexusutils')\n", + "print(nexus_dir)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### **Step 2:** Download APM-specific example data." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "For this case, the data can be found in zenodo." + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import shutil # unpacks in current path unless an additional path argument is provided" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " % Total % Received % Xferd Average Speed Time Time Time Current\n", + " Dload Upload Total Spent Left Speed\n", + "100 127M 100 127M 0 0 1507k 0 0:01:26 0:01:26 --:--:-- 1059k\n" + ] + } + ], + "source": [ + "# http://dx.doi.org/10.5281/zenodo.6808516\n", + "! curl --output APM.LEAP.Datasets.1.zip https://zenodo.org/record/6808516/files/APM.LEAP.Datasets.1.zip\n", + "shutil.unpack_archive('APM.LEAP.Datasets.1.zip')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "These files should serve exclusively as examples. The dataconverter for APM always requires a triplet of files:\n", + "* A **community or vendor file** with the ion positions and mass-to-charge state ratio values for the tomographic reconstruction. POS, ePOS, or APT are allowed.\n", + "* A file with **ranging definitions**, i.e. how mass-to-charge-state ratio values map on ion species. RNG or RRNG are allowed.\n", + "* A **file with additional metadata (edited manually or via an ELN) in YAML format**. The eln_data_apm.yaml file in the example can be edited with a text editor.\n", + "For GUI-based editing, a NOMAD OASIS instance is needed.
\n", + "Please note that the metadata inside the provided eln_data_apm.yaml file has example data in it.\n", + "These reflect not necessarily the conditions when the raw data for the example were given. The file is meant to be edited!" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 3:** Run your APM-specific dataconverter/readers/ on the example data." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we run our parser. The --reader flag takes the atom probe microscopy reader (apm), the --nxdl flag takes the application definition for this technique.
" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Inspect what can/should be in the NeXus file." + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/mkuehbach/SPRINT-9/20221006_refactor_nomad_parser_nexus/nomad-parser-nexus\n" + ] + } + ], + "source": [ + "! echo {nexus_dir}" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### **Step 3a:** Optionally see the command line help of the dataconverter." + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Usage: convert.py [OPTIONS]\n", + "\n", + " The CLI entrypoint for the convert function\n", + "\n", + "Options:\n", + " --input-file TEXT The path to the input data file to read.\n", + " (Repeat for more than one file.)\n", + " --reader [example|apm|transmission|json_map|json_yml|em_nion|ellips|em_spctrscpy|mpes|hall]\n", + " The reader to use. default=\"example\"\n", + " --nxdl TEXT The name of the NXDL file to use without\n", + " extension.\n", + " --output TEXT The path to the output NeXus file to be\n", + " generated.\n", + " --generate-template Just print out the template generated from\n", + " given NXDL file.\n", + " --fair Let the converter know to be stricter in\n", + " checking the documentation.\n", + " --params-file FILENAME Allows to pass a .yaml file with all the\n", + " parameters the converter supports.\n", + " --help Show this message and exit.\n" + ] + } + ], + "source": [ + "! dataconverter --help" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### **Step 3b:** Optionally explore all paths which NXapm provides." + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"/ENTRY[entry]/@version\": \"None\",\n", + " \"/ENTRY[entry]/COORDINATE_SYSTEM_SET[coordinate_system_set]\": \"None\",\n", + " \"/ENTRY[entry]/COORDINATE_SYSTEM_SET[coordinate_system_set]/TRANSFORMATIONS[transformations]\": \"None\",\n", + " \"/ENTRY[entry]/DATA[data]\": \"None\",\n", + " \"/ENTRY[entry]/MONITOR[monitor]\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/address\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/affiliation\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/email\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/name\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/orcid\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/orcid_platform\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/role\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/social_media_name\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/social_media_platform\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/telephone_number\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/REFLECTRON[reflectron]/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/REFLECTRON[reflectron]/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/REFLECTRON[reflectron]/applied\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/REFLECTRON[reflectron]/description\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/REFLECTRON[reflectron]/name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/analysis_chamber/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/analysis_chamber/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/analysis_chamber/description\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/analysis_chamber/name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/analysis_chamber/pressure\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/analysis_chamber/pressure/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/buffer_chamber/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/buffer_chamber/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/buffer_chamber/description\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/buffer_chamber/name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/buffer_chamber/pressure\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/buffer_chamber/pressure/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/control_software/analysis_chamber\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/control_software/buffer_chamber\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/control_software/load_lock_chamber\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/control_software/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/control_software/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/field_of_view\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/field_of_view/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/flight_path_length\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/flight_path_length/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/getter_pump/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/getter_pump/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/getter_pump/design\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/hit_multiplicity/hit_multiplicity\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/hit_multiplicity/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/hit_multiplicity/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/hit_multiplicity/pulse_id\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/hit_multiplicity/pulses_since_last_ion\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/instrument_name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_detector/manufacturer_name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_detector/model\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_detector/name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_detector/serial_number\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_detector/signal_amplitude\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_detector/signal_amplitude/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_detector/type\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_filtering/evaporation_id_included\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_filtering/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_filtering/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_impact_positions/arrival_time_pairs\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_impact_positions/arrival_time_pairs/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_impact_positions/hit_positions\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_impact_positions/hit_positions/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_impact_positions/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ion_impact_positions/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/load_lock_chamber/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/load_lock_chamber/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/load_lock_chamber/description\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/load_lock_chamber/name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/load_lock_chamber/pressure\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/load_lock_chamber/pressure/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/local_electrode/APERTURE_EM[aperture_em]/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/local_electrode/APERTURE_EM[aperture_em]/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/local_electrode/APERTURE_EM[aperture_em]/name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/local_electrode/APERTURE_EM[aperture_em]/value\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/local_electrode/name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/location\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/mass_to_charge_conversion/mass_to_charge\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/mass_to_charge_conversion/mass_to_charge/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/mass_to_charge_conversion/parameter\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/mass_to_charge_conversion/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/mass_to_charge_conversion/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_beam\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_beam/pinhole_position\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_beam/spot_position\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_gun/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_gun/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_gun/name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_gun/power\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_gun/pulse_energy\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/laser_gun/wavelength\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/pulse_fraction\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/pulse_frequency\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/pulse_mode\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/pulsed_voltage\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/pulser/standing_voltage\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/background_quantification/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/background_quantification/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/mass_spectrum/@long_name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/mass_spectrum/bin_ends\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/mass_spectrum/bin_ends/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/mass_spectrum/counts\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/range_increment\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/range_increment/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/range_minmax\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/range_minmax/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/maximum_number_of_atoms_per_molecular_ion\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/number_of_ion_types\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_identification/ION[ion]/charge_state\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_identification/ION[ion]/isotope_vector\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_identification/ION[ion]/mass_to_charge_range\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_identification/ION[ion]/nuclid_list\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_identification/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_identification/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_search_and_deconvolution/PEAK[peak]/label\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_search_and_deconvolution/PEAK[peak]/peak_model\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_search_and_deconvolution/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/peak_search_and_deconvolution/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/ranging/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/crystallographic_calibration\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/@long_name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/counts\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/xpos\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/xpos/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/ypos\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/ypos/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/zpos\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/zpos/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/parameter\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/protocol_name\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/reconstructed_positions\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/reconstruction/reconstructed_positions/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/roughening_pump/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/roughening_pump/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/roughening_pump/design\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/specimen_monitoring/detection_rate\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/specimen_monitoring/detection_rate/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/specimen_monitoring/initial_radius\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/specimen_monitoring/initial_radius/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/specimen_monitoring/shank_angle\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/specimen_monitoring/shank_angle/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/stage_lab/base_temperature\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/stage_lab/base_temperature/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/turbomolecular_pump/FABRICATION[fabrication]/capabilities\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/turbomolecular_pump/FABRICATION[fabrication]/identifier\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/turbomolecular_pump/design\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/voltage_and_bowl_correction/calibrated_tof\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/voltage_and_bowl_correction/calibrated_tof/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/voltage_and_bowl_correction/program\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/voltage_and_bowl_correction/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/voltage_and_bowl_correction/raw_tof\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/voltage_and_bowl_correction/raw_tof/@units\": \"None\",\n", + " \"/ENTRY[entry]/atom_probe/voltage_and_bowl_correction/tof_calibration\": \"None\",\n", + " \"/ENTRY[entry]/definition\": \"None\",\n", + " \"/ENTRY[entry]/end_time\": \"None\",\n", + " \"/ENTRY[entry]/experiment_description\": \"None\",\n", + " \"/ENTRY[entry]/experiment_documentation\": \"None\",\n", + " \"/ENTRY[entry]/experiment_identifier\": \"None\",\n", + " \"/ENTRY[entry]/operation_mode\": \"None\",\n", + " \"/ENTRY[entry]/program\": \"None\",\n", + " \"/ENTRY[entry]/program/@version\": \"None\",\n", + " \"/ENTRY[entry]/run_number\": \"None\",\n", + " \"/ENTRY[entry]/specimen/atom_types\": \"None\",\n", + " \"/ENTRY[entry]/specimen/description\": \"None\",\n", + " \"/ENTRY[entry]/specimen/name\": \"None\",\n", + " \"/ENTRY[entry]/specimen/preparation_date\": \"None\",\n", + " \"/ENTRY[entry]/specimen/sample_history\": \"None\",\n", + " \"/ENTRY[entry]/specimen/short_title\": \"None\",\n", + " \"/ENTRY[entry]/start_time\": \"None\",\n", + " \"/ENTRY[entry]/thumbnail/@type\": \"None\"\n", + "}\n" + ] + } + ], + "source": [ + "# to inspect what can/should all be in the NeXus file\n", + "! dataconverter --nxdl NXapm --generate-template" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### **Step 3c**: Convert the files in the example into an NXapm-compliant NeXus HDF5 file." + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using apm reader to convert the given files: \n", + "• R31_06365-v02.pos\n", + "• R31_06365-v02.rrng\n", + "• eln_data_apm.yaml \n", + "Parsing numerical data and metadata from reconstructed dataset...\n", + "Extracting data from POS file: R31_06365-v02.pos\n", + "Parsing numerical data and metadata from ranging definitions file...\n", + "Extracting data from RRNG file: R31_06365-v02.rrng\n", + "Parsing metadata as well as numerical data from NOMAD OASIS ELN...\n", + "Parsing entry...\n", + "Parsing user...\n", + "Parsing sample...\n", + "Parsing instrument header...\n", + "Parsing fabrication...\n", + "Parsing analysis chamber...\n", + "Parsing reflectron...\n", + "Parsing local electrode...\n", + "Parsing detector...\n", + "Parsing stage_lab...\n", + "Parsing specimen_monitoring...\n", + "Parsing control software...\n", + "Parsing pulser...\n", + "Parsing reconstruction...\n", + "Parsing ranging...\n", + "Creating default plottable data...\n", + "Create default plots on-the-fly...\n", + "--> Enter histogram computation \n", + "(4868202, 3)\n", + "Default plot 3D discretized reconstruction at 1nm binning.\n", + "--> Enter mass spectrum computation \n", + "(4868202, 1)\n", + "Plot mass spectrum at 0.01Da binning was created.\n", + "Forwarding the instantiated template to the NXS writer...\n", + "The path, /ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/@xpos_indices, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/@ypos_indices, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/atom_probe/reconstruction/naive_point_cloud_density_map/DATA[data]/@zpos_indices, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/atom_probe/ranging/mass_to_charge_distribution/mass_spectrum/@bin_ends_indices, is being written but has no documentation.\n", + "The output file generated: usa_pos.nxs\n" + ] + } + ], + "source": [ + "! dataconverter \\\n", + "--reader apm \\\n", + "--nxdl NXapm \\\n", + "--input-file R31_06365-v02.pos \\\n", + "--input-file R31_06365-v02.rrng \\\n", + "--input-file eln_data_apm.yaml \\\n", + "--output usa_pos.nxs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The key take home message is that the command above-specified triggers the automatic creation of the HDF5 file. This *.nxs file, is an HDF5 file." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 4:** Inspect the HDF5/NeXus file apm*.test.nxs using H5Web." + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": {}, + "outputs": [], + "source": [ + "from jupyterlab_h5web import H5Web" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [], + "source": [ + "h5_file_name = 'usa_pos.nxs'" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "data": { + "application/x-hdf5": "/home/mkuehbach/SPRINT-9/20221006_refactor_nomad_parser_nexus/nomad-parser-nexus/examples/apm/usa_pos.nxs", + "text/plain": [ + "" + ] + }, + "execution_count": 34, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "H5Web(h5_file_name)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You can also visualize the .nxs file by double clicking on it in the file explorer panel to the left side of your jupyter lab screen in the browser." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 5:** Optionally, do some post-processing with the generated usa_pos.nxs file." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "To compute a mass-to-charge histogram and explore eventual ranging definitions that have also been carried over in the conversion step (step 6)." + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "from matplotlib.collections import PatchCollection\n", + "from matplotlib.patches import Rectangle\n", + "plt.rcParams['figure.figsize'] = [20, 10]\n", + "plt.rcParams['figure.dpi'] = 300\n", + "import h5py as h5\n", + "#needs shutils for decompressing zip archives, which is a default module/package in Python since >=v3.6" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Read mass-to-charge-state ratio values, create a histogram (\"mass spectrum\"), and mark ranges." + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Array with mass-to-charge-state ratios loaded\n", + "27 iontypes were distinguished\n" + ] + } + ], + "source": [ + "# load data and ranges\n", + "hf = h5.File(h5_file_name, 'r')\n", + "mq = hf['entry/atom_probe/mass_to_charge_conversion/mass_to_charge'][:]\n", + "nions = np.uint32(hf['entry/atom_probe/ranging/number_of_ion_types'])\n", + "print('Array with mass-to-charge-state ratios loaded')\n", + "print(str(nions) + ' iontypes were distinguished')" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Dataset ranging from [0.0, 100.0] Da.\n", + "Using a mass-to-charge-state ratio resolution of 0.01 Da.\n" + ] + } + ], + "source": [ + "# define binning\n", + "[mqmin, mqmax] = [0., 100.0] # Da np.max(mq)]\n", + "print('Dataset ranging from [' + str(mqmin) + ', ' + str(mqmax) +'] Da.')\n", + "mqincr = 0.01 #Da\n", + "print('Using a mass-to-charge-state ratio resolution of '+str(mqincr)+' Da.')" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Histogram has 10001 bins.\n" + ] + } + ], + "source": [ + "# transform collection of mass-to-charge-state ratios into a histogram\n", + "hst1d = np.unique(np.uint64(np.floor((mq[np.logical_and(mq >= mqmin, mq <= mqmax)] - mqmin) / mqincr)), return_counts=True)\n", + "nbins = np.uint64((mqmax - mqmin) / mqincr + 1)\n", + "print('Histogram has ' + str(nbins) + ' bins.')" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Mass-to-charge-state histogram created.\n" + ] + } + ], + "source": [ + "# use matplotlib and numpy to plot histogram data \n", + "xy = np.zeros([nbins, 2], np.float64)\n", + "xy[:,0] = np.linspace(mqmin + mqincr, mqmax + mqincr, nbins, endpoint=True)\n", + "xy[:,1] = 0.5 # * np.ones([nbins], np.float64) # 0.5 to be able to plot logarithm you can not measure half an atom\n", + "for i in np.arange(0, len(hst1d[0])):\n", + " binidx = hst1d[0][i]\n", + " xy[binidx, 1] = hst1d[1][i]\n", + "print('Mass-to-charge-state histogram created.')" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Mass-to-charge-state histogram visualized.\n" + ] + }, + { + "data": { + "text/plain": [ + "(0.5, 10099999.995)" + ] + }, + "execution_count": 40, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "[xmi, xmx, ymi, ymx] = [mqmin, 10**np.ceil(np.log10(mqmax)), 0.5, 10**np.ceil(np.log10(np.max(xy[:,1])))]\n", + "[xmi, xmx, ymi, ymx] = [mqmin, mqmax, 0.5, 10**np.ceil(np.log10(np.max(xy[:,1])))]\n", + "fig, cnts_over_mq = plt.subplots(1, 1)\n", + "plt.plot(xy[:, 0], xy[:, 1], color='blue', alpha=0.5, linewidth=1.0)\n", + "for i in np.arange(1,nions + 1):\n", + " # load ranges and plot them\n", + " ranges = hf['entry/atom_probe/ranging/peak_identification/ion' + str(i) + '/mass_to_charge_range'][:]\n", + " for min_max in ranges:\n", + " cnts_over_mq.vlines(min_max[0], 0, 1, transform=cnts_over_mq.get_xaxis_transform(), alpha=0.1, color='grey', linestyles='dotted')\n", + " cnts_over_mq.vlines(min_max[1], 0, 1, transform=cnts_over_mq.get_xaxis_transform(), alpha=0.1, color='grey', linestyles='dotted')\n", + " #rng = Rectangle((min_max[0], ymi), min_max[1] - min_max[0], ymx - ymi, edgecolor='r', facecolor=\"none\")\n", + "# plt.xticks([1, 2, 3, 4, 5, 6, 7, 8, 9], ['Min', '0.0025', '0.025', '0.25', '0.50', '0.75', '0.975', '0.9975', 'Max'])\n", + "plt.yscale('log')\n", + "plt.legend( [r'Mass-to-charge-state ratio $\\Delta\\frac{m}{q} = $'+str(mqincr)+' Da'], loc='upper right')\n", + "plt.xlabel(r'Mass-to-charge-state-ratio (Da)')\n", + "plt.ylabel(r'Counts')\n", + "print('Mass-to-charge-state histogram visualized.')\n", + "# scale bar with add margin to the bottom and top of the yaxis to avoid that lines fall on x axis\n", + "margin=0.01 # polishing the margins\n", + "plt.xlim([-margin * (xmx - xmi) + xmi, +margin * (xmx - xmi) + xmx])\n", + "plt.ylim([ymi, +margin * (ymx - ymi) + ymx])" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "usa_pos.nxs.MassToChargeStateRatios.png stored to disk.\n" + ] + } + ], + "source": [ + "#save the figure\n", + "figfn = h5_file_name + '.MassToChargeStateRatios.png'\n", + "fig.savefig(figfn, dpi=300, facecolor='w', edgecolor='w', orientation='landscape', format='png', \n", + " transparent=False, bbox_inches='tight', pad_inches=0.1, metadata=None)\n", + "#plt.close('all')\n", + "print(figfn + ' stored to disk.')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Further comments:" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "* Feel free to explore our atom probe microscopy containers in the north branch for more advanced processing" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "### Contact person for this example in FAIRmat:\n", + "Markus Kühbach" + ] + } + ], + "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": "3.8.10" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/tests/data/tools/dataconverter/readers/apm/eln_data_apm.yaml b/examples/apm/eln_data_apm.yaml similarity index 100% rename from tests/data/tools/dataconverter/readers/apm/eln_data_apm.yaml rename to examples/apm/eln_data_apm.yaml diff --git a/examples/ellipsometry/Ellipsometry.NeXus.Example.ipynb b/examples/ellipsometry/Ellipsometry.NeXus.Example.ipynb new file mode 100644 index 000000000..8930a358c --- /dev/null +++ b/examples/ellipsometry/Ellipsometry.NeXus.Example.ipynb @@ -0,0 +1,453 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## DATACONVERTER Demo for Ellipsometry" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 1:** Check that everything is ready to go and download example data." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "check the result of the query below if the modules `jupyterlab_h5web` and `nexusutils` are installed in your environement. Note that next to the name nexusutils you should see the directory in which it is installed. Otherwise make sure that you followed the instructions in the `README` files: \n", + "- how to set up a development environment as in the main README \n", + "- lauch the jupyter lab from this environement as in the README of folder `examples`" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "h5py 3.7.0\n", + "jupyter_client 7.3.5\n", + "jupyter-core 4.11.1\n", + "jupyter-server 1.19.1\n", + "jupyterlab 3.4.8\n", + "jupyterlab-h5web 6.0.1\n", + "jupyterlab-pygments 0.2.2\n", + "jupyterlab_server 2.15.2\n", + "nexusutils 0.0.1 /home/carola/NOMAD/test/nexusutils\n", + "config dir: /home/carola/.jupyter\n", + " jupyterlab_h5web \u001b[32m enabled \u001b[0m\n", + " - Validating...\n", + " jupyterlab_h5web 6.0.1 \u001b[32mOK\u001b[0m\n", + "config dir: /home/carola/NOMAD/npn-test/.pyenv/etc/jupyter\n", + " ipyparallel \u001b[32m enabled \u001b[0m\n", + " - Validating...\n", + " ipyparallel 8.4.1 \u001b[32mOK\u001b[0m\n", + " jupyterlab \u001b[32m enabled \u001b[0m\n", + " - Validating...\n", + " jupyterlab 3.4.8 \u001b[32mOK\u001b[0m\n", + " jupyterlab_h5web \u001b[32m enabled \u001b[0m\n", + " - Validating...\n", + " jupyterlab_h5web 6.0.1 \u001b[32mOK\u001b[0m\n", + "JupyterLab v3.4.8\n", + "/home/carola/.local/share/jupyter/labextensions\n", + " jupyterlab-plotly v5.6.0 \u001b[32menabled\u001b[0m \u001b[32mOK\u001b[0m\n", + "\n", + "/home/carola/NOMAD/npn-test/.pyenv/share/jupyter/labextensions\n", + " jupyterlab_pygments v0.2.2 \u001b[32menabled\u001b[0m \u001b[32mOK\u001b[0m (python, jupyterlab_pygments)\n", + " ipyparallel-labextension v8.4.1 \u001b[32menabled\u001b[0m \u001b[32mOK\u001b[0m\n", + " jupyterlab-h5web v6.0.1 \u001b[32menabled\u001b[0m \u001b[32mOK\u001b[0m (python, jupyterlab_h5web)\n", + "\n", + "Python 3.7.14\n" + ] + } + ], + "source": [ + "! pip list | grep 'h5py\\|nexus\\|jupyter' && jupyter serverextension list && jupyter labextension list && python -V" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Set the nexusutils directory." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Current working directory\n", + "/home/carola/NOMAD/test/nexusutils/examples/ellipsometry\n", + "Base/home/root directory of the nexusutils\n", + "/home/carola/NOMAD/test/nexusutils\n" + ] + } + ], + "source": [ + "import os\n", + "print('Current working directory')\n", + "print(os.getcwd())\n", + "nexus_dir = os.getcwd().replace('/examples/ellipsometry', '')\n", + "# import nexusutils\n", + "# nexus_dir = os.path.dirname(nexusutils.__file__)\n", + "print('Base/home/root directory of the nexusutils')\n", + "print(nexus_dir)" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 2:** Run your example-specific dataconverter/readers/ on the example data." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we run our parser. The --reader flag takes the atom probe microscopy reader (ellips), the --nxdl flag takes the application definition for this technique.
" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Inspect what can/should be in the NeXus file." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/carola/NOMAD/test/nexusutils\n" + ] + } + ], + "source": [ + "! echo {nexus_dir}" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### **Step 2a:** Optionally see the command line help of the dataconverter." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Usage: dataconverter [OPTIONS]\n", + "\n", + " The CLI entrypoint for the convert function\n", + "\n", + "Options:\n", + " --input-file TEXT The path to the input data file to read.\n", + " (Repeat for more than one file.)\n", + " --reader [apm|ellips|em_nion|em_spctrscpy|example|hall|json_map|json_yml|mpes|transmission]\n", + " The reader to use. default=\"example\"\n", + " --nxdl TEXT The name of the NXDL file to use without\n", + " extension.\n", + " --output TEXT The path to the output NeXus file to be\n", + " generated.\n", + " --generate-template Just print out the template generated from\n", + " given NXDL file.\n", + " --fair Let the converter know to be stricter in\n", + " checking the documentation.\n", + " --params-file FILENAME Allows to pass a .yaml file with all the\n", + " parameters the converter supports.\n", + " --help Show this message and exit.\n" + ] + } + ], + "source": [ + "! dataconverter --help" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### **Step 2b:** Optionally explore all paths which the application definition provides." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/detector_type\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/fixed_revolution\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/fixed_revolution/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/intensity_threshold\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/min_intensity\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/other_detector\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/revolution\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/revolution/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/rotating_element\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/DETECTOR[detector]/variable_revolution\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/angle_of_incidence\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/angle_of_incidence/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/angular_spread\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/angular_spread/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/calibration/calibration_data/calibration_angle_of_incidence\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/calibration/calibration_data/calibration_angle_of_incidence/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/calibration/calibration_data/calibration_data\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/calibration/calibration_data/calibration_data_type\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/calibration/calibration_data/calibration_wavelength\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/calibration/calibration_sample\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/calibration/calibration_time\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/calibration_status\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/company\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/construction_year\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/data_correction\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/ellipsometry_type\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/firmware\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/firmware/@url\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/firmware/@version\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/focussing_probes\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/light_source\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/model\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/model/@version\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/GRATING[grating]/angular_dispersion\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/GRATING[grating]/grating_wavelength_max\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/GRATING[grating]/grating_wavelength_max/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/GRATING[grating]/grating_wavelength_min\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/GRATING[grating]/grating_wavelength_min/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/SLIT[slit]/fixed_slit\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/SLIT[slit]/max_gap\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/SLIT[slit]/max_gap/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/spectral_resolution\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/spectral_resolution/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/wavelength\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/spectrometer/wavelength/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/stage/TRANSFORMATIONS[transformations]/alternative\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/stage/description\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/stage/stage_type\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/material\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/orientation_angle\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/orientation_angle/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/other_material\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/reference_data/data\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/reference_data/reference_sample\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/reference_data/reference_wavelength\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/reference_data/reference_wavelength/@units\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/thickness\": \"None\",\n", + " \"/ENTRY[entry]/INSTRUMENT[instrument]/window/thickness/@units\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/atom_types\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/column_names\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/data_error\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/data_identifier\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/data_type\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/SENSOR[sensor]\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/medium\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/medium_refractive_indices\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/number_of_runs\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/number_of_runs/@units\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/optical_excitation/broadening\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/optical_excitation/broadening/@units\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/optical_excitation/duration\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/optical_excitation/duration/@units\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/optical_excitation/pulse_energy\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/optical_excitation/pulse_energy/@units\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/optical_excitation/wavelength\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/optical_excitation/wavelength/@units\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/environment_conditions/varied_parameters\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/layer_structure\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/measured_data\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/preparation_date\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/sample_history\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/sample_name\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/time_points\": \"None\",\n", + " \"/ENTRY[entry]/SAMPLE[sample]/time_points/@units\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/address\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/affiliation\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/email\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/name\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/orcid\": \"None\",\n", + " \"/ENTRY[entry]/USER[user]/telephone_number\": \"None\",\n", + " \"/ENTRY[entry]/acquisition_program/@url\": \"None\",\n", + " \"/ENTRY[entry]/acquisition_program/program\": \"None\",\n", + " \"/ENTRY[entry]/acquisition_program/version\": \"None\",\n", + " \"/ENTRY[entry]/definition\": \"None\",\n", + " \"/ENTRY[entry]/definition/@url\": \"None\",\n", + " \"/ENTRY[entry]/definition/@version\": \"None\",\n", + " \"/ENTRY[entry]/derived_parameters/depolarization\": \"None\",\n", + " \"/ENTRY[entry]/experiment_description\": \"None\",\n", + " \"/ENTRY[entry]/experiment_identifier\": \"None\",\n", + " \"/ENTRY[entry]/plot/@axes\": \"None\",\n", + " \"/ENTRY[entry]/start_time\": \"None\"\n", + "}\n" + ] + } + ], + "source": [ + "# to inspect what can/should all be in the NeXus file\n", + "! dataconverter --nxdl NXellipsometry --generate-template" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### **Step 2c**: Convert the files in the example into a NeXus HDF5 file." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using ellips reader to convert the given files: \n", + "• eln_data.yaml \n", + "The path, /ENTRY[entry]/plot/wavelength, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/wavelength/@units, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/psi_50deg, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/psi_50deg/@units, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/psi_60deg, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/psi_60deg/@units, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/psi_70deg, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/psi_70deg/@units, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/delta_50deg, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/delta_50deg/@units, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/delta_60deg, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/delta_60deg/@units, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/delta_70deg, is being written but has no documentation.\n", + "The path, /ENTRY[entry]/plot/delta_70deg/@units, is being written but has no documentation.\n", + "The output file generated: SiO2onSi.nxs\n" + ] + } + ], + "source": [ + "! dataconverter \\\n", + "--reader ellips \\\n", + "--nxdl NXellipsometry \\\n", + "--input-file eln_data.yaml \\\n", + "--output SiO2onSi.nxs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The key take home message is that the command above-specified triggers the automatic creation of the HDF5 file. This *.nxs file, is an HDF5 file." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 3:** Inspect the HDF5/NeXus file using H5Web." + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [], + "source": [ + "from jupyterlab_h5web import H5Web" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [], + "source": [ + "h5_file_name = 'SiO2onSi.nxs'" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "application/x-hdf5": "/home/carola/NOMAD/test/nexusutils/examples/ellipsometry/SiO2onSi.nxs", + "text/plain": [ + "" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "H5Web(h5_file_name)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You can also visualize the .nxs file by double clicking on it in the file explorer panel to the left side of your jupyter lab screen in the browser." + ] + } + ], + "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": "3.7.14" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/examples/ellipsometry/eln_data.yaml b/examples/ellipsometry/eln_data.yaml new file mode 100644 index 000000000..6b0c7e733 --- /dev/null +++ b/examples/ellipsometry/eln_data.yaml @@ -0,0 +1,71 @@ +acquisition_program/\@url: https://www.jawoollam.com/ellipsometry-software/wvase +acquisition_program/program: WVASE +acquisition_program/version: '3.882' +address: Zum Großen Windkanal 2, 12489 Berlin, Germany +affiliation: Humboldt-Universität zu Berlin +angle_of_incidence_unit: degrees +angular_spread: + unit: rad ** 2 + value: 0.2 +atom_types: Si, O +blocks: +- type +- angle_of_incidence +calibration_status: no calibration +colnames: +- type +- wavelength +- angle_of_incidence +- psi +- delta +- err.psi +- err.delta +column_names: +- psi +- delta +company: J. A. Woollam Co. +count_time: + unit: s + value: 1 +data_identifier: 1 +data_type: psi/delta +definition: NXellipsometry +definition/\@url: https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat-ellips/contributed_definitions/NXellipsometry.nxdl.xml +definition/\@version: 0.0.2 +detector_type: CCD spectrometer +ellipsometry_type: dual compensator +email: surname.name@physik.hu-berlin.de +err-var: +- err.psi +- err.delta +experiment_description: RC2 scan on 2nm SiO2 on Si in air +experiment_identifier: exp-ID +filename: test-data.dat +firmware: CompleteEASE +firmware/\@url: https://www.jawoollam.com/ellipsometry-software/completeease +firmware/\@version: '6.37' +focussing_probes: false +integration_time: + unit: s + value: 0 +layer_structure: 2nm SiO2 on Si +light_source: arc lamp +medium: air +model: RC2 +model/\@version: 0.0.1 +name: Name Surname +parameters: +- type +- angle +rotating_element: compensator (source side) +sample_history: Commercially purchased sample +sample_name: 2nm SiO2 on Si +sep: \t +skip: 3 +stage_type: manual stage +start_time: '2022-01-27T04:35:00+00:00' +wavelength_unit: angstrom +x-var: wavelength +y-var: +- psi +- delta diff --git a/tests/data/tools/dataconverter/readers/ellips/test-data.dat b/examples/ellipsometry/test-data.dat similarity index 100% rename from tests/data/tools/dataconverter/readers/ellips/test-data.dat rename to examples/ellipsometry/test-data.dat diff --git a/tests/data/tools/dataconverter/readers/em_spctrscpy/EmSpctrscpy.NeXus.NXem.Example.1.ipynb b/examples/em/EmSpctrscpy.NeXus.NXem.Example.1.ipynb similarity index 79% rename from tests/data/tools/dataconverter/readers/em_spctrscpy/EmSpctrscpy.NeXus.NXem.Example.1.ipynb rename to examples/em/EmSpctrscpy.NeXus.NXem.Example.1.ipynb index 9b7306690..d5c832bdb 100644 --- a/tests/data/tools/dataconverter/readers/em_spctrscpy/EmSpctrscpy.NeXus.NXem.Example.1.ipynb +++ b/examples/em/EmSpctrscpy.NeXus.NXem.Example.1.ipynb @@ -16,15 +16,45 @@ "### **Step 1:** Check that everything is ready to go and download example data for EDS/STEM, EELS/TEM." ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "check the result of the query below if the modules `jupyterlab_h5web` and `nexusutils` are installed in your environement. Note that next to the name nexusutils you should see the directory in which it is installed. Otherwise make sure that you followed the instructions in the `README` files: \n", + "- how to set up a development environment as in the main README \n", + "- lauch the jupyter lab from this environement as in the README of folder `examples`" + ] + }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "! pip list | grep 'nomad\\|nexus'\n", - "! jupyter serverextension list\n", - "! jupyter labextension list" + "! pip list | grep 'h5py\\|nexus\\|jupyter' && jupyter serverextension list && jupyter labextension list && python -V" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Set nexus directory." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "print('Current working directory')\n", + "print(os.getcwd())\n", + "nexus_dir = os.getcwd().replace('/examples/em', '')\n", + "# import nexusutils\n", + "# nexus_dir = os.path.dirname(nexusutils.__file__)\n", + "print('Base/home/root directory of the nomad-parser-nexus')\n", + "print(nexus_dir)" ] }, { @@ -76,25 +106,6 @@ "### **Step 3:** Run your EM-spectroscopy-specific dataconverter/readers/ on the example data." ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Set the nexusparser directory." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import os\n", - "import nexusparser\n", - "nexus_dir = os.path.dirname(nexusparser.__file__)\n", - "print(nexus_dir)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -108,7 +119,7 @@ "metadata": {}, "outputs": [], "source": [ - "! python3 {nexus_dir}/tools/dataconverter/convert.py --help" + "! dataconverter --help" ] }, { @@ -124,7 +135,7 @@ "metadata": {}, "outputs": [], "source": [ - "! python3 {nexus_dir}/tools/dataconverter/convert.py --nxdl NXem --reader em_spctrscpy --generate-template" + "! dataconverter --nxdl NXem --reader em_spctrscpy --generate-template" ] }, { @@ -143,7 +154,7 @@ "#parser-nexus/tests/data/tools/dataconverter/readers/em/\n", "numerical_data = [\"46_ES-LP_L1_brg.bcf\", \"1613_Si_HAADF_610_kx.emd\", \"EELS_map_2_ROI_1_location_4.dm3\"]\n", "output_file_name = [\"epfl_bcf.nxs\", \"epfl_emd.nxs\", \"hu_dm3.nxs\"]\n", - "! python3 {nexus_dir}/tools/dataconverter/convert.py \\\n", + "! dataconverter \\\n", "--reader em_spctrscpy \\\n", "--nxdl NXem \\\n", "--input-file EELS_map_2_ROI_1_location_4.dm3 \\\n", @@ -208,6 +219,14 @@ "***" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Contact person for this example in FAIRmat:\n", + "Markus Kühbach" + ] + }, { "cell_type": "code", "execution_count": null, @@ -218,7 +237,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3.7.11 ('nomad_north')", "language": "python", "name": "python3" }, @@ -232,7 +251,12 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.10" + "version": "3.7.11" + }, + "vscode": { + "interpreter": { + "hash": "fb9c1bd38c7663f011bf442e740f4844d912585f80182885cfafffa0a1ff37a6" + } } }, "nbformat": 4, diff --git a/tests/data/tools/dataconverter/readers/em_spctrscpy/eln_data_em.yaml b/examples/em/eln_data_em.yaml similarity index 100% rename from tests/data/tools/dataconverter/readers/em_spctrscpy/eln_data_em.yaml rename to examples/em/eln_data_em.yaml diff --git a/examples/mpes/mpes.NeXus.mpes.Example.1.ipynb b/examples/mpes/mpes.NeXus.mpes.Example.1.ipynb new file mode 100644 index 000000000..dc05ad89d --- /dev/null +++ b/examples/mpes/mpes.NeXus.mpes.Example.1.ipynb @@ -0,0 +1,223 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## nexusutils demo for Multidimensional Photoemission Spectroscopy (MPES)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Jupyter notebook displaying parsing from FHI preprocessing software output (x-array based .h5) to NXmpes formatted nexus" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 1:** Check that everything is ready to go and download example data. " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "check the result of the query below if the modules `jupyterlab_h5web` and `nexusutils` are installed in your environement. Note that next to the name nexusutils you should see the directory in which it is installed. Otherwise make sure that you followed the instructions in the `README` files: \n", + "- how to set up a development environment as in the main README \n", + "- lauch the jupyter lab from this environement as in the README of folder `examples`" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "! pip list | grep 'h5py\\|nexus\\|jupyter' && jupyter serverextension list && jupyter labextension list && python -V" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Download mpes example data from Zenodo" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "! curl -o MoTe_xarray_final.h5 https://zenodo.org/record/5913599/files/MoTe_xarray_final.h5?download=1" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 2:** Run your mpes-specific parser on the example data" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Set the nexusparser directory." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "print('Current working directory')\n", + "print(os.getcwd())\n", + "nexus_dir = os.getcwd().replace('/examples/mpes', '')\n", + "# import nexusutils\n", + "# nexus_dir = os.path.dirname(nexusutils.__file__)\n", + "print('Base/home/root directory of the nexusutils')\n", + "print(nexus_dir)\n", + "data_dir = nexus_dir + '/tests/data/dataconverter/readers/mpes/'" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now we run our parser. The --reader flag takes the mpes reader (mpes), the --nxdl flag takes the application definition for this technique.
" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "! dataconverter \\\n", + "--reader mpes \\\n", + "--nxdl NXmpes \\\n", + "--input-file MoTe_xarray_final.h5 \\\n", + "--input-file {data_dir}config_file.json \\\n", + "--input-file {data_dir}ELN_metadata_example.yaml \\\n", + "--output mpes.test.nxs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Run the same parser alternatively using a function " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from nexusutils.dataconverter.convert import convert" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "convert(input_file=[\"MoTe_xarray_final.h5\", data_dir + \"config_file.json\", data_dir + \"ELN_metadata_example.yaml\"],\n", + " reader='mpes',\n", + " nxdl='NXmpes',\n", + " output='mpes.test.nxs')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The key take home message is that the command above-specified triggers the automatic creation of the HDF5 file.
\n", + "This *.nxs file, is an HDF5 file." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "tags": [] + }, + "source": [ + "### **Step 3:** Inspect the HDF5/NeXus file using H5Web" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from jupyterlab_h5web import H5Web" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "h5_file_name = 'mpes.test.nxs'" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "H5Web(h5_file_name)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "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": "3.7.11" + }, + "vscode": { + "interpreter": { + "hash": "fb9c1bd38c7663f011bf442e740f4844d912585f80182885cfafffa0a1ff37a6" + } + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/tests/data/tools/dataconverter/readers/mpes/mpes.WSe2.Binning2NeXus.mpes.Example.2.ipynb b/examples/mpes/mpes.WSe2.Binning2NeXus.mpes.Example.2.ipynb similarity index 100% rename from tests/data/tools/dataconverter/readers/mpes/mpes.WSe2.Binning2NeXus.mpes.Example.2.ipynb rename to examples/mpes/mpes.WSe2.Binning2NeXus.mpes.Example.2.ipynb diff --git a/nexusparser.yaml b/nexusparser.yaml deleted file mode 100644 index 0bfd855b3..000000000 --- a/nexusparser.yaml +++ /dev/null @@ -1,7 +0,0 @@ -# NexusParser Parameter File - v0.0.1 - -dataconverter: - reader: mpes - output: output.nxs - nxdl: NXmpes - input-file: ['config_file.json', 'ELN_metadata_example.yaml', 'xarray_saved_small_calibration.h5'] \ No newline at end of file diff --git a/nexusparser/metadata.yaml b/nexusparser/metadata.yaml deleted file mode 100644 index 3b918850d..000000000 --- a/nexusparser/metadata.yaml +++ /dev/null @@ -1,64 +0,0 @@ -codeName: nexus -codeLabel: NeXus -codeCategory: Database manager -status: production -codeLabelStyle: 'capitals: N, X.' -codeUrl: https://www.nexusformat.org/ -parserDirName: dependencies/parsers/nexus/ -parserGitUrl: https://github.com/nomad-coe/nomad-parser-nexus.git -preamble: | - This is not a real parser, but an example template on how to write one. You can fork this repository to create actual parsers. - - ## Get started - - You should create a virtual environment. This is optional, but highly recommended as - the required nomad-lab pypi package requires many dependencies with specific versions - that might conflict with other libraries that you have installed. This was tested - with Python 3.7. - - ``` - pip install virtualenv - virtualenv -p `which python3` .pyenv - source .pyenv/bin/activate - ``` - - Simply install our pypi package with pip: - ``` - pip install --upgrade pip - pip install nomad-lab - ``` - - Clone this project (or fork and then clone the fork). Go into the cloned directly and - directly run the parser from there: - ``` - git clone https://github.com/nomad-coe/nomad-parser-nexus.git parser-nexus - cd parser-nexus - python -m nexusparser tests/data/nexus.out - ``` - - There are also a basic test framework written in [pytest](https://docs.pytest.org/en/stable/). - Install the remaining dev dependencies and run the tests with: - ``` - pip install -r requirements.txt - pytest -sv tests - ``` - - ## Next steps - - Our documentation provides several resources that might be interesting: - - [How to write a parser](https://nomad-lab.eu/prod/rae/docs/parser.html). Provides - a more detailed tutorial on how to write a parser. - - [Introduction to the NOMAD Metainfo](https://nomad-lab.eu/prod/rae/docs/metainfo.html). - This explains how NOMAD data schema and can be extended and used within your parser. - - To get you parser included in NOMAD or ask further questions, you can: - - Use our forums at [matsci.org](https://matsci.org/c/nomad/32) - - Open an issue on the [nexus-parser GitHub project](https://github.com/nomad-coe/nomad-parser-nexus/issues) - - Write to [support@nomad-lab.eu](mailto:support@nomad-lab.eu) - - **Note!** The rest of this README.md is the usual text that applies to all NOMAD parsers. - -tableOfFiles: | - |Input Filename| Description| - |--- | --- | - |`nexus.out` | **Mainfile** in NEXUS specific plain-text | diff --git a/nexusparser/metainfo/nexus.py b/nexusparser/metainfo/nexus.py deleted file mode 100644 index 38e8ae425..000000000 --- a/nexusparser/metainfo/nexus.py +++ /dev/null @@ -1,544 +0,0 @@ -"""This tool is reading the xml file - -""" -# -# 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. -# - -import re -import os -import os.path -import sys -from typing import Dict, Any -import xml.etree.ElementTree as ET -import numpy as np -from nomad.utils import strip -from nomad.metainfo import ( - Section, Package, SubSection, Definition, Datetime, Bytes, Unit, MEnum, Quantity) -from nomad.datamodel import EntryArchive -from nexusparser.tools import nexus - -# URL_REGEXP from -# https://stackoverflow.com/questions/3809401/what-is-a-good-regular-expression-to-match-a-url -URL_REGEXP = re.compile(r'(https?:\/\/(www\.)?[-a-zA-Z0-9@:%._\+~#=]' - r'{1,256}\.[a-zA-Z0-9()]{1,6}\b([-a-zA-Z0-9()@:%_\+.~#?&//=]*))') -XML_NAMESPACES = {'nx': 'http://definition.nexusformat.org/nxdl/3.1'} - -# TO DO the validation still show some problems. Most notably there are a few higher -# dimensional fields with non number types, which the metainfo does not support -VALIDATE = False -CURRENT_PACKAGE: Package = None -_definition_sections: Dict[str, Section] = dict() -_XML_PARENT_MAP: Dict[ET.Element, ET.Element] = None -_NX_DOC_BASE = 'https://manual.nexusformat.org/classes' -_NX_TYPES = { # Primitive Types, 'ISO8601' is the only type not defined here - 'NX_COMPLEX': np.dtype(np.float64), - 'NX_FLOAT': np.dtype(np.float64), - 'NX_CHAR': str, - 'NX_BOOLEAN': bool, - 'NX_INT': np.dtype(np.int64), - 'NX_UINT': np.dtype(np.uint64), - 'NX_NUMBER': np.dtype(np.number), - 'NX_POSINT': np.dtype(np.uint64), - 'NX_BINARY': Bytes, - 'NX_DATE_TIME': Datetime} - - -def to_camel_case(snake_str: str, upper: bool = False): - """Take as input a snake case variable and return a camel case one - -""" - components = snake_str.split('_') - - if upper: - return ''.join(f'{x[0].upper()}{x[1:]}' for x in components) - - return components[0] + ''.join(f'{x[0].upper()}{x[1:]}' for x in components[1:]) - - -def nx_documenation_url(xml_node: ET.Element, nx_type: str): - """Get documentation url - -""" - anchor_segments = [] - if nx_type != 'class': - anchor_segments.append(nx_type) - - while xml_node is not None: - xml_parent = xml_node - if 'name' in xml_node.attrib: - anchor_segments.append(xml_node.attrib['name'].replace('_', '-')) - else: - anchor_segments.append(xml_node.attrib['type'][2:].replace('_', '-')) - - xml_node = _XML_PARENT_MAP.get(xml_node) - - anchor = "-".join([name.lower() for name in reversed(anchor_segments)]) - nx_package = xml_parent.get('nxdl_base').split('/')[-1] - doc_url = f'{_NX_DOC_BASE}/{nx_package}/{anchor_segments[-1]}.html#{anchor}' - return doc_url - - -def get_or_create_section(name: str, **kwargs) -> Section: - """Returns the 'existing' metainfo section for a given top-level nexus base-class name. - - This function ensures that sections for these base-classes are only created one. - This allows to access the metainfo section even before it is generated from the base-class - nexus definition. - -""" - if name in _definition_sections: - section = _definition_sections[name] - section.more.update(**kwargs) - return section - - section = Section(validate=VALIDATE, name=name, **kwargs) - CURRENT_PACKAGE.section_definitions.append(section) - _definition_sections[section.name] = section - - return section - - -def get_enum(xml_node: ET.Element): - """Get the enumeration field from xml node - -""" - enumeration = xml_node.find('nx:enumeration', XML_NAMESPACES) - if enumeration is not None: - enum_values = [] - for enum_value in enumeration.findall('nx:item', XML_NAMESPACES): - enum_values.append(enum_value.attrib['value']) - return MEnum(*enum_values) - return None - - -def add_common_properties_helper(base_section, definition): - """Define definition var from base_section var - -""" - if base_section.description: - definition.description = base_section.description - if base_section.deprecated: - definition.deprecated = base_section.deprecated - if base_section.more: - definition.more.update(**base_section.more) - - -def get_nexus_category(xml_node: ET.Element): - ''' - retrieves the category from the root element - ''' - elem = xml_node - parent = elem - while parent is not None: - elem = parent - parent = _XML_PARENT_MAP.get(elem) - return elem.attrib['category'] - - -def add_common_properties(xml_node: ET.Element, definition: Definition): - ''' - Adds general metainfo definition properties (e.g. deprecated, docs, optional, ...) - from the given nexus XML node to the given metainfo definition. - ''' - nx_kind = definition.more.get('nx_kind') - nx_category = get_nexus_category(xml_node) - xml_attrs = xml_node.attrib - - # Read properties from potential base section. Those are not inherited, but we - # duplicate them for a nicer presentation - if isinstance(definition, Section) and definition.base_sections: - base_section = definition.base_sections[0] - add_common_properties_helper(base_section, definition) - links = [] - if nx_kind is not None: - doc_url = nx_documenation_url(xml_node, nx_kind) - if doc_url: - links.append(doc_url) - - doc = xml_node.find('nx:doc', XML_NAMESPACES) - if doc is not None and doc.text is not None: - definition.description = strip(doc.text) - for match in URL_REGEXP.findall(definition.description): - links.append(match[0]) - - if links: - definition.links = links - - if 'deprecated' in xml_attrs: - definition.deprecated = xml_attrs['deprecated'] - - definition.more['nx_optional'] = xml_attrs.get( - 'optional', nx_category == 'base') - - if 'minOccurs' in xml_attrs: - definition.more['nx_min_occurs'] = xml_attrs['minOccurs'] - if 'maxOccurs' in xml_attrs: - definition.more['nx_max_occurs'] = xml_attrs['maxOccurs'] - if 'required' in xml_attrs: - definition.more['nx_required'] = xml_attrs['required'] - if 'recommended' in xml_attrs: - definition.more['nx_recommended'] = xml_attrs['recommended'] - - if 'category' in xml_attrs: - definition.more['nx_category'] = xml_attrs['category'] - - # TO DO there are probably even more nxdl attributes? - - -def add_attributes(xml_node: ET.Element, section: Section): - ''' - Adds quantities for all attributes in the given nexus XML node to the given - section. - ''' - for attribute in xml_node.findall('nx:attribute', XML_NAMESPACES): - attribute_section = create_attribute_section(attribute, section) - - name = attribute.attrib["name"] - max_occurs = attribute.attrib.get('maxOccurs', '0') - repeats = any(name_char.isupper() - for name_char in name) or max_occurs == 'unbounded' or int(max_occurs) > 1 - - section.sub_sections.append(SubSection( - section_def=attribute_section, nx_kind='attribute', - name=f'nx_attribute_{name}', repeats=repeats)) - - -def add_group_properties(xml_node: ET.Element, section: Section): - ''' - Adds all properties that can be generated from the given nexus group XML node to - the given (empty) metainfo section definition. - ''' - for group in xml_node.findall('nx:group', XML_NAMESPACES): - group_section = create_group_section(group, section) - section.inner_section_definitions.append(group_section) - if 'name' in group.attrib: - name = f'nx_group_{group.attrib["name"]}' - else: - name = f'nx_group_{group.attrib["type"].replace("NX", "").upper()}' - max_occurs = group.attrib.get('maxOccurs', '0') - repeats = any(name_char.isupper() - for name_char in name) or max_occurs == 'unbounded' or int(max_occurs) > 1 - section.sub_sections.append(SubSection( - section_def=group_section, nx_kind='group', name=name, repeats=repeats)) - for field in xml_node.findall('nx:field', XML_NAMESPACES): - field_section = create_field_section(field, section) - name = field.attrib["name"] - max_occurs = field.attrib.get('maxOccurs', '0') - repeats = any(name_char.isupper() - for name_char in name) or max_occurs == 'unbounded' or int(max_occurs) > 1 - - section.sub_sections.append(SubSection( - section_def=field_section, nx_kind='field', - name=f'nx_field_{name}', repeats=repeats)) - - add_attributes(xml_node, section) - - -def add_template_properties(xml_node: ET.Element, section: Section): - ''' - Adds potential abilities of a group or field section to act as a TEMPLATE or - nameType="any" definition. - ''' - is_template = section.name.lower() != section.name or 'name' not in xml_node.attrib - if is_template: - section.quantities.append(Quantity( - name='nx_name', type=str, default=xml_node.attrib.get('name'), description=''' - This is a nexus template property. This quantity holds the actual name used - in the nexus data.''')) - - -def add_base_section(section: Section, container: Section, default_base_section: Section = None): - ''' - Potentially adds a base section to the given section, if the given container has - a base-section with a suitable base. - ''' - base_section = container.all_inner_section_definitions.get(section.name, None) - if base_section: - assert base_section.nx_kind == section.nx_kind, 'base section has wrong nexus kind' - else: - base_section = default_base_section - - if base_section: - section.base_sections = [base_section] - - -def create_attribute_section(xml_node: ET.Element, container: Section) -> Section: - ''' - Creates a metainfo section from the nexus attribute given as xml node. - ''' - xml_attrs = xml_node.attrib - assert 'name' in xml_attrs, 'attribute has not name' - - attribute_section = Section( - validate=VALIDATE, nx_kind='attribute', - name=xml_attrs['name'] + 'Attribute') - add_base_section(attribute_section, container) - container.inner_section_definitions.append(attribute_section) - - base_value_quantity = attribute_section.all_quantities.get('nx_value') - if base_value_quantity is None: - value_quantity = Quantity( - name='nx_value', description='The value for this nexus attribute') - else: - value_quantity = base_value_quantity.m_copy() - attribute_section.quantities.append(value_quantity) - - enum_type = get_enum(xml_node) - if enum_type is not None: - value_quantity.type = enum_type - - if value_quantity.type is None: - value_quantity.type = str - - add_common_properties(xml_node, attribute_section) - add_template_properties(xml_node, attribute_section) - - return attribute_section - - -def add_units(xml_attrs, field_section): - """add units to section""" - if 'units' in xml_attrs: - field_section.more['nx_units'] = xml_attrs['units'] - if xml_attrs['units'] != 'NX_UNITLESS': - # TO DO a default could be created from the nx_units value - field_section.quantities.append(Quantity( - name='nx_unit', type=Unit, - # a_elasticsearch=Elasticsearch(), - description='The specific unit for that this fields data has.')) - return field_section - - -def create_field_section(xml_node: ET.Element, container: Section): - ''' - Creates a metainfo section from the nexus field given as xml node. - ''' - xml_attrs = xml_node.attrib - - assert 'name' in xml_attrs, 'field has not name' - name = xml_attrs['name'] + 'Field' - field_section = Section(validate=VALIDATE, nx_kind='field', name=name) - add_base_section(field_section, container) - container.inner_section_definitions.append(field_section) - - add_template_properties(xml_node, field_section) - - base_value_quantity = field_section.all_quantities.get('nx_value') - if base_value_quantity: - value_quantity = base_value_quantity.m_copy() - else: - value_quantity = Quantity(name='nx_value', description='The value for this nexus field') - field_section.quantities.append(value_quantity) - - if 'type' in xml_attrs: - nx_type = xml_attrs['type'] - else: - nx_type = 'NX_CHAR' - if nx_type not in _NX_TYPES: - raise NotImplementedError(f'type {nx_type} is not supported for {name}') - field_section.more['nx_type'] = nx_type - - if value_quantity.type is None or value_quantity.type is Any or nx_type != 'NX_CHAR': - value_quantity.type = _NX_TYPES[nx_type] - - enum_type = get_enum(xml_node) - if enum_type: - value_quantity.type = enum_type - - if value_quantity.type is None: - value_quantity.type = Any - - field_section = add_units(xml_attrs, field_section) - - dimensions = xml_node.find('nx:dimensions', XML_NAMESPACES) - if dimensions is not None: - shape = [] - for dimension in dimensions.findall('nx:dim', XML_NAMESPACES): - dimension_value: Any = dimension.attrib.get('value', '*') - try: - dimension_value = int(dimension_value) - except ValueError: - pass - shape.append(dimension_value) - value_quantity.shape = shape - - add_common_properties(xml_node, field_section) - add_attributes(xml_node, field_section) - - return field_section - - -def create_group_section(xml_node: ET.Element, container: Section) -> Section: - ''' - Creates a metainfo section from the nexus group given as xml node. - ''' - xml_attrs = xml_node.attrib - typ = xml_attrs['type'] - - if 'name' in xml_attrs: - name = xml_attrs['name'] + 'Group' - else: - name = typ + 'Group' - - group_section = Section(validate=VALIDATE, nx_kind='group', name=name) - add_base_section(group_section, container, get_or_create_section(typ)) - - add_common_properties(xml_node, group_section) - add_template_properties(xml_node, group_section) - add_group_properties(xml_node, group_section) - - return group_section - - -def create_class_section(xml_node: ET.Element) -> Section: - ''' - Creates a metainfo section from the top-level nexus definition given as xml node. - ''' - xml_attrs = xml_node.attrib - assert 'name' in xml_attrs - assert 'category' in xml_attrs - - class_section = get_or_create_section(xml_attrs['name'], - nx_kind=xml_attrs['type'], - nx_category=xml_attrs['category']) - - if 'extends' in xml_attrs: - base_section = get_or_create_section(xml_attrs['extends']) - class_section.base_sections = [base_section] - - add_common_properties(xml_node, class_section) - add_group_properties(xml_node, class_section) - - return class_section - - -def sort_nxdl_files(paths): - '''sorting all definitions based on dependencies''' - def compare_dependencies(nxdl1, nxdl2): - if 'extends' in nxdl1.attrib and nxdl1.attrib['extends'] == nxdl2.attrib['name']: - return True - for group1 in nxdl1.iter("*"): - if group1.tag[group1.tag.rindex("}") + 1:] == 'group' and \ - group1.attrib['type'] == nxdl2.attrib['name']: - break - else: - return False - for group2 in nxdl2.iter("*"): - if group2.tag[group2.tag.rindex("}") + 1:] == 'group' and \ - group2.attrib['type'] == nxdl1.attrib['name']: - return False - return True - - list_of_nxdl = [] - for path in paths: - for nxdl_file in sorted(os.listdir(path)): - if not nxdl_file.endswith('.nxdl.xml'): - continue - if nxdl_file in [el.attrib["name"] + '.nxdl.xml' for el in list_of_nxdl]: - continue - xml_tree = ET.parse(os.path.join(path, nxdl_file)) - xml_node = xml_tree.getroot() - xml_node.set('nxdl_base', path) - assert xml_node.attrib.get('type') == 'group', 'definition is not a group' - list_of_nxdl.append(xml_node) - sorted_index = 0 - while sorted_index < len(list_of_nxdl): - current_index = sorted_index + 1 - while current_index < len(list_of_nxdl): - if compare_dependencies(list_of_nxdl[sorted_index], list_of_nxdl[current_index]): - list_of_nxdl.append(list_of_nxdl[sorted_index]) - list_of_nxdl.__delitem__(sorted_index) - break - current_index = current_index + 1 - if current_index == len(list_of_nxdl): - sorted_index = sorted_index + 1 - # print('\n'.join([(nxdl.attrib['name'],p.attrib["nxdl_base"]) for nxdl in list_of_nxdl])) - return list_of_nxdl - - -def add_section_from_nxdl(xml_node): - ''' - Creates a metainfo section from an nxdl file. - ''' - try: - global _XML_PARENT_MAP # pylint: disable=global-statement - _XML_PARENT_MAP = { - child: parent for parent in xml_node.iter() for child in parent} - - # The section gets already implicitly added to CURRENT_PACKAGE by get_or_create_section - create_class_section(xml_node) - - except NotImplementedError as err: - print('Exception while mapping ' + xml_node.attrib["name"] + ':', err, file=sys.stderr) - - -def create_package_from_nxdl_directories(paths) -> Package: - ''' - Creates a metainfo package from the given nexus directory. Will generate the respective - metainfo definitions from all the nxdl files in that directory. - ''' - global CURRENT_PACKAGE # pylint: disable=global-statement - CURRENT_PACKAGE = Package(name=f'nexus') - - sorted_files = sort_nxdl_files(paths) - for nxdl_file in sorted_files: - add_section_from_nxdl(nxdl_file) - - return CURRENT_PACKAGE - - -# separated metainfo package for the nexus base classes, application defs and contributed classes. -DIRS = [os.path.join(nexus.get_nexus_definitions_path(), 'contributed_definitions')] -DIRS.append(os.path.join(nexus.get_nexus_definitions_path(), 'base_classes')) -DIRS.append(os.path.join(nexus.get_nexus_definitions_path(), 'applications')) -APPLICATIONS = create_package_from_nxdl_directories(DIRS) -PACKAGES = (APPLICATIONS,) # , APPLICATIONS, CONTRIBUTED) - -# We take the application definitions and create a common parent section that allows to -# include nexus in an EntryArchive. -NEXUS_SECTION = Section(validate=VALIDATE, name='Nexus') - -for application_section in APPLICATIONS.section_definitions: # pylint: disable=not-an-iterable - if application_section.more.get('nx_category') == 'application': - sub_section = SubSection( - section_def=application_section, - name=application_section.name.replace('NX', 'nx_application_')) - NEXUS_SECTION.sub_sections.append(sub_section) - -APPLICATIONS.section_definitions.append(NEXUS_SECTION) - -ENTRY_ARCHIVE_NEXUS_SUB_SECTION = \ - SubSection(name='nexus', - section_def=NEXUS_SECTION) -EntryArchive.nexus = ENTRY_ARCHIVE_NEXUS_SUB_SECTION # type: ignore -EntryArchive.m_def.sub_sections.append(ENTRY_ARCHIVE_NEXUS_SUB_SECTION) -ENTRY_ARCHIVE_NEXUS_SUB_SECTION.init_metainfo() - - -# We need to initialize the metainfo definitions. This is usually done automatically, -# when the metainfo schema is defined though MSection Python classes. -for package in PACKAGES: - package.init_metainfo() - - -# We skip the Python code generation for now and offer Python classes as variables -# TO DO not necessary right now, could also be done case-by-case by the nexus parser -PYTHON_MODULE = sys.modules[__name__] -for package in PACKAGES: - for sektion in package.section_definitions: # pylint: disable=not-an-iterable - setattr(PYTHON_MODULE, sektion.name, sektion.section_cls) diff --git a/nexusparser/parser.py b/nexusparser/parser.py deleted file mode 100644 index c926578c9..000000000 --- a/nexusparser/parser.py +++ /dev/null @@ -1,288 +0,0 @@ -"""parser doc - -""" -# -# 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. -# - -from typing import Iterable, Union -import os -import pathlib -import numpy as np -from nomad.datamodel import EntryArchive -from nomad.parsing import MatchingParser -# from . import metainfo # pylint: disable=unused-import -from nexusparser.tools import nexus as read_nexus -from nexusparser.metainfo import nexus - - -def get_to_new_subsection(hdf_name, nxdef, nxdl_node, act_section): - """hdf_name name of the hdf group/field/attribute (None for definition) - nxdef application definition - nxdl_node node in the nxdl.xml - act_class actual class - act_section actual section in which the new entry needs to be picked up from - Note that if the new element did not exists, it is created now - return (new_class, new_section) - TODO: try to find also in the base section??? - -""" - if hdf_name is None: - nomad_def_name = 'nx_application_' + nxdef[2:] - # nomad_class_name = nxdef - elif nxdl_node.tag.endswith('field'): - nxdl_f_a_name = nxdl_node.attrib['name'] if 'name' in nxdl_node.attrib else hdf_name - nomad_def_name = 'nx_field_' + nxdl_f_a_name - # nomad_class_name = self.get_nomad_classname(nxdl_f_a_name, None, "Field") - elif nxdl_node.tag.endswith('group'): - nxdl_g_name = nxdl_node.attrib['name'] \ - if 'name' in nxdl_node.attrib else nxdl_node.attrib['type'][2:].upper() - nomad_def_name = 'nx_group_' + nxdl_g_name - # nomad_class_name = self.get_nomad_classname(read_nexus.get_node_name(nxdl_node), - # nxdl_node.attrib['type'], "Group") - else: - nxdl_f_a_name = nxdl_node.attrib['name'] if 'name' in nxdl_node.attrib else hdf_name - nomad_def_name = 'nx_attribute_' + nxdl_f_a_name - # nomad_class_name = self.get_nomad_classname(nxdl_f_a_name, None, "Attribute") - - new_def = act_section.m_def.all_sub_sections[nomad_def_name] - new_class = new_def.section_def.section_cls - new_section = None - for section in act_section.m_get_sub_sections(new_def): - if hdf_name is None or (getattr(section, "nx_name") and section.nx_name == hdf_name): - new_section = section - break - if new_section is None: - act_section.m_create(new_class) - new_section = act_section.m_get_sub_section(new_def, -1) - if hdf_name is not None: - new_section.nx_name = hdf_name - return (new_class, new_section) - - -def get_value(hdf_node): - """Get value from hdl5 node - -""" - hdf_value = hdf_node[...] - if str(hdf_value.dtype) == 'bool': - val = bool(hdf_value) - elif hdf_value.dtype.kind in 'iufc': - val = hdf_value - else: - try: - val = str(hdf_value.astype(str)) - except UnicodeDecodeError: - val = str(hdf_node[()].decode()) - return val - - -def helper_nexus_populate(nxdl_attribute, act_section, val, logger): - """Handle info of units attribute, raise error if default or something else is found - -""" - try: - if nxdl_attribute == "units": - act_section.nx_unit = val[0] - elif nxdl_attribute == "default": - Exception("Quantity 'default' is not yet added by default to groups in Nomad schema") - except Exception as exc: # pylint: disable=broad-except - logger.debug("Problem with storage!!!\n" + str(exc)) - - -def nexus_populate_helper(params): - """helper for nexus_populate""" - (path_level, nxdl_path, act_section, logstr, val, loglev, nxdef, hdf_node) = params - if path_level < len(nxdl_path): - nxdl_attribute = nxdl_path[path_level] - if isinstance(nxdl_attribute, str): - # conventional attribute not in schema. Only necessary, - # if schema is not populated according - # helper_nexus_populate(nxdl_attribute, act_section, val, logger) - try: - if nxdl_attribute == "units": - act_section.nx_unit = val[0] - elif nxdl_attribute == "default": - Exception( - "'default' is not yet added by default to groups in Nomad schema") - except Exception as exc: # pylint: disable=broad-except - logstr += ("Problem with storage!!!\n" + str(exc)) + '\n' - loglev = 'error' - else: - # attribute in schema - act_section = \ - get_to_new_subsection(nxdl_attribute.attrib['name'], nxdef, - nxdl_attribute, act_section)[1] - try: - act_section.nx_value = val[0] - except (AttributeError, TypeError, ValueError) as exc: - logstr += ("Problem with storage!!!\n" + str(exc)) + '\n' - loglev = 'error' - else: - try: - data_field = get_value(hdf_node) - if hdf_node[...].dtype.kind in 'iufc' and \ - isinstance(data_field, np.ndarray) and \ - data_field.size > 1: - data_field = np.array([ - np.mean(data_field), - np.var(data_field), - np.min(data_field), - np.max(data_field) - ]) - act_section.nx_value = data_field - except (TypeError, ValueError) as exc: - logstr += ("Problem with storage!!!\n" + str(exc)) + '\n' - loglev = 'error' - return [logstr, loglev] - - -def add_log(params, logstr): - """adds log entry for the given node""" - if params["nxdef"] is not None: - logstr += params["nxdef"] - else: - logstr += '???' - logstr += ':' - first = True - for p_node in params["nxdl_path"]: - if first: - first = False - else: - logstr += '.' - if isinstance(p_node, str): - logstr += p_node - else: - read_nexus.get_node_name(p_node) - logstr += ' - ' + params["val"][0] - if len(params["val"]) > 1: - logstr += '...' - logstr += '\n' - return logstr - - -class NexusParser(MatchingParser): - ''' - NexusParser doc - ''' - - def __init__(self): - super().__init__( - metadata_path=f'{pathlib.Path(__file__).parent.resolve()}/metadata.yaml', - mainfile_mime_re=r'(application/.*)|(text/.*)', - mainfile_name_re=(r'.*\.nxs'), - supported_compressions=['gz', 'bz2', 'xz'] - ) - self.archive = None - self.nxroot = None - - def is_mainfile( # pylint: disable=too-many-arguments - self, filename: str, mime: str, buffer: bytes, decoded_buffer: str, - compression: str = None) -> Union[bool, Iterable[str]]: - accepted_extensions = (".nxs", ".yaml", ".yml") - extension = pathlib.Path(filename).suffix - if extension in accepted_extensions: - if buffer[0:8] == b'\x89HDF\r\n\x1a\n': - return True - if buffer[0:30] == b"# NexusParser Parameter File -": - return True - return False - -# def get_nomad_classname(self, xml_name, xml_type, suffix): -# """Get nomad classname from xml file - -# """ -# if suffix == 'Attribute' or suffix == 'Field' or xml_type[2:].upper() != xml_name: -# name = xml_name + suffix -# else: -# name = xml_type + suffix -# return name - - def nexus_populate(self, params, attr=None): - """Walks through hdf_namelist and generate nxdl nodes - (hdf_info, nxdef, nxdl_path, val, logger) = params""" - hdf_path = params["hdf_info"]['hdf_path'] - hdf_node = params["hdf_info"]['hdf_node'] - logstr = hdf_path + (("@" + attr) if attr else '') + '\n' - loglev = 'info' - if params["nxdl_path"] is not None: - logstr = add_log(params, logstr) - act_section = self.nxroot - hdf_namelist = hdf_path.split('/')[1:] - act_section = get_to_new_subsection(None, params["nxdef"], None, act_section)[1] - path_level = 1 - for hdf_name in hdf_namelist: - if path_level < len(params["nxdl_path"]): - nxdl_node = params["nxdl_path"][path_level] - else: - nxdl_node = hdf_name - act_section = get_to_new_subsection(hdf_name, params["nxdef"], - nxdl_node, act_section)[1] - path_level += 1 - helper_params = (path_level, params["nxdl_path"], act_section, logstr, params["val"], - loglev, params["nxdef"], hdf_node) - (logstr, loglev) = nexus_populate_helper(helper_params) - else: - logstr += ('NOT IN SCHEMA - skipped') + '\n' - loglev = 'warning' - if loglev == 'info': - params["logger"].info('Parsing', nexusparser=logstr) - elif loglev == 'warning': - params["logger"].warning('Parsing', nexusparser=logstr) - elif loglev == 'error': - params["logger"].error('Parsing', nexusparser=logstr) - else: - params["logger"].critical('Parsing', nexusparser=logstr + 'NOT HANDLED\n') - - def parse(self, mainfile: str, archive: EntryArchive, logger=None, child_archives=None): - self.archive = archive - self.archive.m_create(nexus.Nexus) # type: ignore[attr-defined] # pylint: disable=no-member - self.nxroot = self.archive.nexus - - extension = pathlib.Path(mainfile).suffix - if extension in (".yaml", ".yml"): - base_dir = os.path.dirname(mainfile) - from nexusparser.tools.dataconverter.convert import convert, parse_params_file - with open(mainfile) as file: - conv_params = parse_params_file(file) - - def check_path(path: str): - """Return true if path supplied by the user is not absolute or has a ../""" - if os.path.isabs(path) or ".." in path: - raise Exception("The user provided an invalid path in the parameter YAML.") - return path - - if isinstance(conv_params["input_file"], list): - conv_params["input_file"] = [f"{base_dir}{os.sep}{check_path(file)}" - for file in conv_params["input_file"]] - else: - conv_params["input_file"] = (f"{base_dir}{os.sep}" - f"{check_path(conv_params['input_file'])}") - conv_params["output"] = f"{base_dir}{os.sep}{check_path(conv_params['output'])}" - convert(**conv_params) - mainfile = conv_params["output"] - - nexus_helper = read_nexus.HandleNexus(logger, [mainfile]) - nexus_helper.process_nexus_master_file(self.nexus_populate) - - appdef = "" - for var in dir(archive.nexus): - if var.startswith("nx_application") and getattr(archive.nexus, var) is not None: - appdef = var[len("nx_application_"):] - - if archive.metadata is not None: - archive.metadata.entry_type = f"NX{appdef}" diff --git a/nexusparser/tools/__init__.py b/nexusparser/tools/__init__.py deleted file mode 100644 index 792d60054..000000000 --- a/nexusparser/tools/__init__.py +++ /dev/null @@ -1 +0,0 @@ -# diff --git a/nexusparser/tools/dataconverter/readers/README.md b/nexusparser/tools/dataconverter/readers/README.md deleted file mode 100644 index c82b5e28e..000000000 --- a/nexusparser/tools/dataconverter/readers/README.md +++ /dev/null @@ -1,87 +0,0 @@ -# File/Metadata and Data Format Reader Plug-ins aka ``reader`` - -The purpose of the dataconverter is to create HDF5 files with content that matches a specific NeXus application definition. -Such application definitions are useful for collecting a set of pieces of information about a specific experiment in a given -scientific field. The pieces of information are metadata and numerical data. The application definition is used to provide -these data in a format that the duties of a data delivery contract can be fulfilled: The HDF5 file, or so-called NeXus file, -delivers all those pieces of information which the application definition specifies. - -The here developed and so-called readers, are effectively software tools (plug-ins) which the converter calls to -accomplish this task for a specific set of application definition (NXDL file) plus a set of experiment/method-specific file(s). -These files can be files in a proprietary format, or of a certain format used in the respective scientific community, or -text files. Only in combination these files hold at least all the required pieces of information which the -application definition demands. - -## Project structure - -- `tbd` - Maybe further explanations are useful here. - -## Getting started - -The readers get cloned as plug-in dependencies while cloning the dataconverter. -Therefore, please follow the instructions for cloning the reader as a complete package. - -## Download the example data for testing and development purposes - -Before using your own data we strongly encourage you to download a set of open-source -test data for testing the plug-ins. There are specific jupyter-notebook examples (where??) which -detail how these tests can be executed for each of the specific readers which are listed below. - -Once you have practised with these tools how to convert these examples, feel free to -use the tools for converting your own data. You should feel invited to contact the respective -corresponding author(s) of each plug-in if you run into issues with the plug-in or feel there -is a necessity to include additional data into the NeXus file for the respective application. - -We are looking forward for learning from your experience and see the interesting use cases. - -## Current readers/plug-ins - -Details to the individual readers follow. Each reader is documented with a description -of its primary target audience, its scientific field and corresponding author. In addition, -individual support is given on how each reader can be executed. - -## apm - -`targets:` atom probe microscopy -`accepts:` NXapm.nxdl.xml -`offers:` generic reader for atom probe tomography and some related field-ion microscopy experiments. -`supports:` pos, epos, apt (the one introduced with AP Suite), rng, rrng, json -`statusquo:` single experiment + single range file + single file with additional metadata as a json document. -`contact:` Markus Kühbach (Humboldt-Universität zu Berlin) - -```sh -python converter.py --reader apm --nxdl ../../definitions/applications/NXapm.nxdl.xml --input-file 70_50_50.apt --input-file SeHoKim_R5076_44076_v02.rng --input-file ManuallyCollectedMetadata.json --output apm.test.nxs -``` - -## arpes - -`targets:` photo-emission spectroscopy -`accepts:` ?? -`offers:` ?? -`supports:` ?? -`statusquo:` ?? -`contact:` Tommaso Pincelli, Laurenz Rettig, Abeer Arora (Fritz-Haber-Institute of the Max-Planck Society) - -## em_nion - -`targets:` electron microscopy -`accepts:` NXem_nion.nxdl.xml -`offers:` initial reader for results from Nion microscopes and results achieved with nionswift software. -`supports:` npy, json -`statusquo:` single experiment and two json file(s) with additional metadata -`contact:` Markus Kühbach, Benedikt Haas, Sherjeel Shabih (Humboldt-Universität zu Berlin) - -```sh -python converter.py --reader em_nion --nxdl ../../definitions/applications/NXem_nion.nxdl.xml --input-file HAADF_01.npy --input-file HAADF_01.json --input-file HAADF_01.ELabFTW.dat --output em.test.nxs -``` - -## ellipsometry - -`targets:` ellipsometry -`accepts:` ?? -`offers:` ?? -`supports:` ?? -`statusquo:` ?? -`contact:` Carola Emminger, Tamas Haraszti, Chris Sturm (add affiliations) - - diff --git a/nexusparser/__init__.py b/nexusutils/__init__.py similarity index 100% rename from nexusparser/__init__.py rename to nexusutils/__init__.py diff --git a/nexusparser/tools/dataconverter/Readme.md b/nexusutils/dataconverter/README.md similarity index 77% rename from nexusparser/tools/dataconverter/Readme.md rename to nexusutils/dataconverter/README.md index 3590349da..2c16acee6 100644 --- a/nexusparser/tools/dataconverter/Readme.md +++ b/nexusutils/dataconverter/README.md @@ -1,6 +1,6 @@ -# Data Converter +# Dataconverter -Converts experimental data to Nexus/HDF5 files based on any provided NXDL. +Converts experimental data to NeXus/HDF5 files based on any provided NXDL. ```console user@box:~$ python convert.py @@ -12,7 +12,7 @@ Options: --reader TEXT The reader to use. --nxdl TEXT The name of the NXDL file to use without extension. [required] - --output TEXT The path to the output Nexus file to be generated. + --output TEXT The path to the output NeXus file to be generated. --generate-template Just print out the template generated from given NXDL file. @@ -30,6 +30,7 @@ user@box:~$ python convert.py --nxdl nxdl --input_file metadata --input_file dat 1, Clone the repo using: `git clone https://github.com/nomad-coe/nomad-parser-nexus.git --recursive`\ 2. From the root folder where the setup.py exists, run: pip install -e . +Sherjeel, check here the correct repo to checkout, should not be data-converter as this may no longer exist ```console user@box:~$ git clone https://github.com/nomad-coe/nomad-parser-nexus.git --recursive user@box:~$ cd nomad-parser-nexus @@ -38,13 +39,14 @@ user@box:~$ pip install -e . user@box:~$ cd nexusparser/tools/dataconverter ``` -For now, I have made sure that this tools works on this branch. - ## Writing a Reader -This converter allows extending support to other data formats by allowing extensions called readers. The converter provides a dev platform to build a Nexus compatible reader by providing checking against a chosen Nexus Application Definition. +This converter allows extending support to other data formats by allowing extensions called readers. +The converter provides a dev platform to build a NeXus compatible reader by providing checking +against a chosen NeXus Application Definition. -Readers have to be placed in the **readers** folder in there own subfolder. The reader folder should be named with the reader's name and contain a `reader.py`.\ +Readers have to be placed in the **readers** folder in there own subfolder. +The reader folder should be named with the reader's name and contain a `reader.py`.\ For example: The reader `Example Reader` is placed under `dataconverter/readers/example/reader.py`. Copy and rename `readers/example/reader.py` to your own `readers/mydatareader/reader.py`. @@ -52,14 +54,14 @@ Copy and rename `readers/example/reader.py` to your own `readers/mydatareader/re Then implement the reader function: ```python -"""MyDataReader implementation for the DataConverter to convert mydata to Nexus.""" +"""MyDataReader implementation for the DataConverter to convert mydata to NeXus.""" from typing import Tuple, Any -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader +from dataconverter.readers.base.reader import BaseReader class MyDataReader(BaseReader): - """MyDataReader implementation for the DataConverter to convert mydata to Nexus.""" + """MyDataReader implementation for the DataConverter to convert mydata to NeXus.""" def read( self, @@ -82,10 +84,14 @@ READER = MyDataReader ``` -The read function takes a template dictionary based on the provided NXDL file (similar to `--generate-template`) and the list of all the file paths the user provides with `--input`. -The returned dictionary should contain keys that exist in the template as defined below. The values of these keys have to be data objects to be populated in the output Nexus file. They can be lists, numpy arrays, numpy bytes, numpy floats, numpy ints. Practically you can pass any value that can be handled by `h5py` package. +The read function takes a template dictionary based on the provided NXDL file (similar to `--generate-template`) +and the list of all the file paths the user provides with `--input`. +The returned dictionary should contain keys that exist in the template as defined below. +The values of these keys have to be data objects to be populated in the output NeXus file. +They can be lists, numpy arrays, numpy bytes, numpy floats, numpy ints. Practically you can pass any value +that can be handled by the `h5py` package. -Then you can then call this using: +The dataconverter can be executed using: ```console user@box:~$ dataconverter --reader mydata --nxdl NXmynxdl --output path_to_output.nxs @@ -111,7 +117,7 @@ Example: ``` In case the NXDL does not define a `name` for the group the requested data belongs to, the template dictionary will list it as `/NAME_IN_NXDL[name_in_output_nexus]` -You can choose any name you prefer instead of the suggested name. This allows the reader function to repeat groups defined in the NXDL to be outputted to the Nexus file. +You can choose any name you prefer instead of the suggested name. This allows the reader function to repeat groups defined in the NXDL to be outputted to the NeXus file. ```json { diff --git a/nexusparser/tools/dataconverter/__init__.py b/nexusutils/dataconverter/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/__init__.py rename to nexusutils/dataconverter/__init__.py diff --git a/nexusparser/tools/dataconverter/convert.py b/nexusutils/dataconverter/convert.py similarity index 93% rename from nexusparser/tools/dataconverter/convert.py rename to nexusutils/dataconverter/convert.py index 3d2c46c5b..054e886b6 100644 --- a/nexusparser/tools/dataconverter/convert.py +++ b/nexusutils/dataconverter/convert.py @@ -15,7 +15,7 @@ # See the License for the specific language governing permissions and # limitations under the License. # -"""This script runs the conversion routine using a selected reader and write out a Nexus file.""" +"""This script runs the conversion routine using a selected reader and write out a NeXus file.""" import glob import importlib.machinery import importlib.util @@ -28,11 +28,11 @@ import click import yaml -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader -from nexusparser.tools.dataconverter import helpers -from nexusparser.tools.dataconverter.writer import Writer -from nexusparser.tools.dataconverter.template import Template -from nexusparser.tools import nexus +from nexusutils.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter import helpers +from nexusutils.dataconverter.writer import Writer +from nexusutils.dataconverter.template import Template +from nexusutils.nexus import nexus logger = logging.getLogger(__name__) # pylint: disable=C0103 @@ -75,7 +75,7 @@ def convert(input_file: Tuple[str], # Reading in the NXDL and generating a template definitions_path = nexus.get_nexus_definitions_path() if nxdl == "NXtest": - nxdl_path = os.path.join("tests", "data", "tools", "dataconverter", "NXtest.nxdl.xml") + nxdl_path = os.path.join("tests", "data", "dataconverter", "NXtest.nxdl.xml") elif nxdl == "NXroot": nxdl_path = os.path.join(definitions_path, "base_classes", "NXroot.nxdl.xml") else: @@ -160,7 +160,7 @@ def parse_params_file(params_file): @click.option( '--output', default='output.nxs', - help='The path to the output Nexus file to be generated.' + help='The path to the output NeXus file to be generated.' ) @click.option( '--generate-template', @@ -194,7 +194,7 @@ def convert_cli(input_file: Tuple[str], except TypeError: sys.tracebacklimit = 0 raise Exception(("Please make sure you have the following entries in your " - "parameter file:\n\n# NexusParser Parameter File - v0.0.1" + "parameter file:\n\n# NeXusParser Parameter File - v0.0.1" "\n\ndataconverter:\n\treader: value\n\tnxdl: value\n\tin" "put-file: value")) else: diff --git a/nexusparser/tools/dataconverter/convert_routine.svg b/nexusutils/dataconverter/convert_routine.svg similarity index 99% rename from nexusparser/tools/dataconverter/convert_routine.svg rename to nexusutils/dataconverter/convert_routine.svg index b8de1ffd6..3cf339023 100644 --- a/nexusparser/tools/dataconverter/convert_routine.svg +++ b/nexusutils/dataconverter/convert_routine.svg @@ -1,3 +1,3 @@ -
convert.py
convert.py
Generate Template
Generate Template
--nxdl
--nxdl
The NXDL used for conversion.
The NXDL used for...
Select Reader
Select Reader
--reader
--reader
The reader ID sent in from the command line.
The reader ID sent...
Reader Data
Reader Data
The flat dictionary sent back by the read func.
The flat dictionar...
Call the writer function
Call the writer funct...
--input_file (1..n)
--input_file (1....
The input data file paths sent in from the command line.
The input data fil...
--output
--output
The output filename
The output filen...
Output Nexus file
Output Nexus file
Call the read func of selected reader
Call the read func of...Viewer does not support full SVG 1.1 \ No newline at end of file +
convert.py
convert.py
Generate Template
Generate Template
--nxdl
--nxdl
The NXDL used for conversion.
The NXDL used for...
Select Reader
Select Reader
--reader
--reader
The reader ID sent in from the command line.
The reader ID sent...
Reader Data
Reader Data
The flat dictionary sent back by the read func.
The flat dictionar...
Call the writer function
Call the writer funct...
--input_file (1..n)
--input_file (1....
The input data file paths sent in from the command line.
The input data fil...
--output
--output
The output filename
The output filen...
Output NeXus file
Output NeXus file
Call the read func of selected reader
Call the read func of...Viewer does not support full SVG 1.1 \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/helpers.py b/nexusutils/dataconverter/helpers.py similarity index 98% rename from nexusparser/tools/dataconverter/helpers.py rename to nexusutils/dataconverter/helpers.py index 43565d3b3..d46b5862c 100644 --- a/nexusparser/tools/dataconverter/helpers.py +++ b/nexusutils/dataconverter/helpers.py @@ -23,8 +23,8 @@ import numpy as np -from nexusparser.tools import nexus -from nexusparser.tools.nexus import NxdlAttributeError +from nexusutils.nexus import nexus +from nexusutils.nexus.nexus import NxdlAttributeError def is_a_lone_group(xml_element) -> bool: @@ -90,12 +90,12 @@ def get_required_string(elem): def convert_nexus_to_caps(nexus_name): - """Helper function to convert a Nexus class from to .""" + """Helper function to convert a NeXus class from to .""" return nexus_name[2:].upper() def convert_nexus_to_suggested_name(nexus_name): - """Helper function to suggest a name for a group from its Nexus class.""" + """Helper function to suggest a name for a group from its NeXus class.""" return nexus_name[2:] diff --git a/nexusutils/dataconverter/readers/README.md b/nexusutils/dataconverter/readers/README.md new file mode 100644 index 000000000..f9a8c08f0 --- /dev/null +++ b/nexusutils/dataconverter/readers/README.md @@ -0,0 +1,45 @@ +# File/Metadata and Data Format Reader Plug-ins aka ``reader`` + +The purpose of the dataconverter is to create NeXus/HDF5 files with content that +matches a specific NeXus application definition. +Such application definitions are useful for collecting a set of pieces of information +about a specific experiment in a given scientific field. The pieces of information +are metadata and numerical data. The application definition is used to provide +these data in a format that serves a data delivery contract: The HDF5 file, +or so-called NeXus file, delivers all those pieces of information which the +application definition specifies. Required and optional pieces of information are +distinguished. NeXus classes can recommend the inclusion of certain pieces of information. +Recommended data are essentially optional. The idea is that flagging these data as +recommended motivates users to collect them but does not require to write dummy +or nonsense data if the user is unable to collect recommended data. + +The here developed and so-called readers, are effectively software tools (plug-ins) +which the converter calls to accomplish this task for a specific set of application +definition (NXDL XML file) plus a set of experiment/method-specific file(s). +These files can be files in a proprietary format, or of a certain format used in the +respective scientific community, or text files. Only in combination, these files hold +all the required pieces of information which the application definition demands and which +are thus required to make a NeXus/HDF5 file compliant. Users can store additional +pieces of information in an NeXus/HDF5 file. In this case readers will issue a warning +that these data are not properly documented from the perspective of NeXus. + +## Getting started + +The readers get cloned as plug-in dependencies while cloning the dataconverter. +Therefore, please follow the instructions for cloning the reader as a complete package. + +## Download the example data for testing and development purposes + +Before using your own data we strongly encourage you to download a set of open-source +test data for testing the plug-ins. For this purpose the nomad-parser-nexus comes with +a tests directory with a data/dataconverter sub-directory including reader-specific jupyter-notebook +examples. These examples can be used for downloading test data and use specific readers +as a standalone converter to translate given data into a NeXus/HDF5 file. + +Once you have practised with these tools how to convert these examples, feel free to +use the tools for converting your own data. You should feel invited to contact the respective +corresponding author(s) of each reader if you run into issues with the reader or feel there +is a necessity to include additional data into the NeXus file for the respective application. + +We are looking forward for learning from your experience and see the interesting use cases. +You can find the contact persons in the respective README.md of each reader. diff --git a/nexusparser/tools/dataconverter/readers/__init__.py b/nexusutils/dataconverter/readers/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/__init__.py rename to nexusutils/dataconverter/readers/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/apm/README.md b/nexusutils/dataconverter/readers/apm/README.md similarity index 73% rename from nexusparser/tools/dataconverter/readers/apm/README.md rename to nexusutils/dataconverter/readers/apm/README.md index 0845921b2..de457fd42 100644 --- a/nexusparser/tools/dataconverter/readers/apm/README.md +++ b/nexusutils/dataconverter/readers/apm/README.md @@ -1,16 +1,18 @@ # APM reader ## Purpose -Translate diverse vendor and community file formats from atom probe microscopy into -a standardized representation using the NeXus application definition NXapm. -This parser does not copy over all of the data and metadata in the vendor file(s) -but the particular subset which is understood and useful inside a NOMAD OASIS instance. +Translate diverse file formats from the scientific community and technology partners +within the field of atom probe microscopy into a standardized representation using the +NeXus application definition NXapm. +This parser does not copy over all of the data and metadata in file(s) from technology +partners like Cameca/AMETEK but only the particular subset which is understood and +useful inside a NOMAD OASIS instance. ## What this apm reader supports The main idea behind the parser is to offer users of the OASIS a diverse example of how a parser for specific file formats can be written and designed. We would like to encourage the APM community to share example files with us. These can be small and come from diverse use cases. -Ideally, these should represent data in vendor file formats other than the already supported +Ideally, these should represent data in files other than the already supported ones, so that we can broaden the applicability of this parser. Specifically, the implementation shows how data and metadata in different file formats can @@ -27,21 +29,21 @@ provided also these export a YAML file using the same formatting. ## Getting started - usage related to NOMAD OASIS This parser can be used to map numerical data and metadata inside frequently -used vendor file formats of electron microscopy software tools into a NeXus +used file formats of electron microscopy software tools into a NeXus HDF5 file which complies with a specific version of the NXapm application definition. If you are using a NOMAD OASIS, you can use this tool as follows. 1. Log-in to a NOMAD OASIS and navigate to the *Create Upload* tab. 2. Select APM example from the list of available options. -3. Drag-and-drop your files in vendor-specific formats, i.e. pos, epos, apt +3. Drag-and-drop your files in specific formats, i.e. pos, epos, apt (for reconstructed datasets) and rrng or rng (for ranging definitions/range files). 3. Edit the electronic lab notebook (ELN) schema inside the NOMAD OASIS and click the save button in the NOMAD OASIS GUI to save the data that you have entered into the ELN template. Clicking *save* will trigger the automatic generation of an eln_data.yaml file. Second, the clicking will trigger a run of the dataconverter/apm parser which generates a NXapm NeXus file based on the data - in the vendor file and the eln_data.yaml file. Afterwards, the file will be + in the file and the eln_data.yaml file. Afterwards, the file will be displayed in the GUI and upload section of your OASIS. By default the converter performs a strong loss-less compression on the input as many of the stack data store integers with a low entropy. @@ -56,7 +58,7 @@ If you are using a NOMAD OASIS, you can use this tool as follows. ## Getting started - standalone usage If you use this dataconverter/apm parser as a standalone tool, 1. You should follow the interactive jupyter notebook that is stored in - *nomad-parser-nexus\tests\data\tools\dataconverter\readers\apm*. + *nomad-parser-nexus/tests/data/dataconverter/readers\apm*. 2. As the standalone usage of this parser does not require a NOMAD OASIS instance, you have to edit the ELN manually or via another ELN. For this you can edit the example eln_data_apm.yaml which comes shipped with this example. Alternatively, @@ -68,25 +70,24 @@ If you use this dataconverter/apm parser as a standalone tool, into an instance of a NeXus HDF5 file that is formatted according to the NXapm application definition. -## A request to take action by the vendors -In fact, while the above-mentioned vendor file formats and corresponding vendor software is routinely +## A request to take action by the technology partners +In fact, while the above-mentioned file formats and corresponding commercial software is routinely used by numerous atom probers every day, the actual knowledge about the I/O routines has always -been on a few developers shoulders. In fact many of the open-source readers for vendor file formats were -reverse-engineered. This is challenging because the amount of documentation that is especially -for some vendor file formats available is neither exhaustive nor detailed enough. This limits developers +been on a few developers shoulders. In fact many of the open-source readers for file formats were +reverse-engineered. This is challenging because the amount of documentation that is available +for some file formats is neither exhaustive nor documented enough in detail. This limits developers to decide and design how to best implement possible mappings of specific binary numerical data and metadata -into specifically named fields. We wish that intensified exchange between vendors and the community -can help to improve the situation. Everybody is very welcomed to leave us comments in the issue -list to exchange specifically about this topic. +into specifically named fields. We wish that intensified exchange between technology partners like +AMETEK/Cameca and the atom probe community can help to improve the situation. +Everybody is very welcomed to leave us comments in the issue list (or drop us an email) +to exchange specifically about this topic. -Limited technical documentation of some vendor file formats stands in strong contrast -to the powerful GUI-based tools and the in fact continuous efforts of the vendors -to make the barriers for working with microscopy data simpler and becoming more -aligned with the FAIR principles. - -## Known limitations of this parser +## Known limitations of this reader Currently the apm parser reads the following quantities: reconstructed ion positions, and mass-to-charge-state ratio values. The readers are technically capable to read also all other fields in ePOS and APT files to the extent as these have been documented. + +## Contact person in FAIRmat for this reader +Markus Kühbach diff --git a/nexusparser/tools/dataconverter/readers/apm/__init__.py b/nexusutils/dataconverter/readers/apm/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/__init__.py rename to nexusutils/dataconverter/readers/apm/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/apm/reader.py b/nexusutils/dataconverter/readers/apm/reader.py similarity index 89% rename from nexusparser/tools/dataconverter/readers/apm/reader.py rename to nexusutils/dataconverter/readers/apm/reader.py index 347081698..7ea98748d 100644 --- a/nexusparser/tools/dataconverter/readers/apm/reader.py +++ b/nexusutils/dataconverter/readers/apm/reader.py @@ -24,21 +24,21 @@ from typing import Tuple, Any -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.readers.base.reader import BaseReader -from nexusparser.tools.dataconverter.readers.apm.utils.apm_use_case_selector \ +from nexusutils.dataconverter.readers.apm.utils.apm_use_case_selector \ import ApmUseCaseSelector -from nexusparser.tools.dataconverter.readers.apm.utils.apm_reconstruction_io \ +from nexusutils.dataconverter.readers.apm.utils.apm_reconstruction_io \ import ApmReconstructionParser -from nexusparser.tools.dataconverter.readers.apm.utils.apm_ranging_io \ +from nexusutils.dataconverter.readers.apm.utils.apm_ranging_io \ import ApmRangingDefinitionsParser -from nexusparser.tools.dataconverter.readers.apm.utils.apm_nomad_oasis_eln_io \ +from nexusutils.dataconverter.readers.apm.utils.apm_nomad_oasis_eln_io \ import NxApmNomadOasisElnSchemaParser -from nexusparser.tools.dataconverter.readers.apm.utils.apm_nexus_plots \ +from nexusutils.dataconverter.readers.apm.utils.apm_nexus_plots \ import apm_default_plot_generator # each reconstruction should be stored as an own file because for commercial diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/NXapmInformationSourcesToNeXus.ods b/nexusutils/dataconverter/readers/apm/utils/NXapmInformationSourcesToNeXus.ods similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/NXapmInformationSourcesToNeXus.ods rename to nexusutils/dataconverter/readers/apm/utils/NXapmInformationSourcesToNeXus.ods diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/__init__.py b/nexusutils/dataconverter/readers/apm/utils/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/__init__.py rename to nexusutils/dataconverter/readers/apm/utils/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/apm_nexus_base_classes.py b/nexusutils/dataconverter/readers/apm/utils/apm_nexus_base_classes.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/apm_nexus_base_classes.py rename to nexusutils/dataconverter/readers/apm/utils/apm_nexus_base_classes.py diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/apm_nexus_plots.py b/nexusutils/dataconverter/readers/apm/utils/apm_nexus_plots.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/apm_nexus_plots.py rename to nexusutils/dataconverter/readers/apm/utils/apm_nexus_plots.py diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/apm_nomad_oasis_eln_io.py b/nexusutils/dataconverter/readers/apm/utils/apm_nomad_oasis_eln_io.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/apm/utils/apm_nomad_oasis_eln_io.py rename to nexusutils/dataconverter/readers/apm/utils/apm_nomad_oasis_eln_io.py index 0372a78fe..a6bc69cff 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/apm_nomad_oasis_eln_io.py +++ b/nexusutils/dataconverter/readers/apm/utils/apm_nomad_oasis_eln_io.py @@ -32,10 +32,10 @@ from ase.data import chemical_symbols -# from nexusparser.tools.dataconverter.readers.apm.utils.apm_nexus_base_classes \ +# from nexusutils.dataconverter.readers.apm.utils.apm_nexus_base_classes \ # import NxObject -from nexusparser.tools.dataconverter.readers.apm.utils.apm_versioning \ +from nexusutils.dataconverter.readers.apm.utils.apm_versioning \ import NX_APM_ADEF_NAME, NX_APM_ADEF_VERSION, NX_APM_EXEC_NAME, NX_APM_EXEC_VERSION diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/apm_ranging_io.py b/nexusutils/dataconverter/readers/apm/utils/apm_ranging_io.py similarity index 97% rename from nexusparser/tools/dataconverter/readers/apm/utils/apm_ranging_io.py rename to nexusutils/dataconverter/readers/apm/utils/apm_ranging_io.py index fcb0777b9..24aeba334 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/apm_ranging_io.py +++ b/nexusutils/dataconverter/readers/apm/utils/apm_ranging_io.py @@ -26,13 +26,13 @@ import numpy as np -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_utils \ import unhash_isotope # , hash_isotope -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_rng_reader \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_rng_reader \ import ReadRngFileFormat -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_rrng_reader \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_rrng_reader \ import ReadRrngFileFormat diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/apm_reconstruction_io.py b/nexusutils/dataconverter/readers/apm/utils/apm_reconstruction_io.py similarity index 96% rename from nexusparser/tools/dataconverter/readers/apm/utils/apm_reconstruction_io.py rename to nexusutils/dataconverter/readers/apm/utils/apm_reconstruction_io.py index a98c41d69..3290dbf5c 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/apm_reconstruction_io.py +++ b/nexusutils/dataconverter/readers/apm/utils/apm_reconstruction_io.py @@ -24,13 +24,13 @@ import numpy as np -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_apt6_reader \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_apt6_reader \ import ReadAptFileFormat -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_pos_reader \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_pos_reader \ import ReadPosFileFormat -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_epos_reader \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_epos_reader \ import ReadEposFileFormat diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/apm_use_case_selector.py b/nexusutils/dataconverter/readers/apm/utils/apm_use_case_selector.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/apm_use_case_selector.py rename to nexusutils/dataconverter/readers/apm/utils/apm_use_case_selector.py diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/apm_versioning.py b/nexusutils/dataconverter/readers/apm/utils/apm_versioning.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/apm_versioning.py rename to nexusutils/dataconverter/readers/apm/utils/apm_versioning.py diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_headers.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_headers.py similarity index 98% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_headers.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_headers.py index dc8475f5d..77935cc22 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_headers.py +++ b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_headers.py @@ -24,7 +24,7 @@ import numpy as np -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_apt6_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_apt6_utils \ import string_to_typed_nparray # , np_uint16_to_string diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_reader.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_reader.py similarity index 96% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_reader.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_reader.py index 7a40a4e30..5e23ff468 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_reader.py +++ b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_reader.py @@ -32,15 +32,15 @@ # from pint import UnitRegistry -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_apt6_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_apt6_utils \ import np_uint16_to_string -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_apt6_headers \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_apt6_headers \ import AptFileHeaderMetadata -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_apt6_sections \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_apt6_sections \ import AptFileSectionMetadata -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_apt6_sections_branches \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_apt6_sections_branches \ import EXPECTED_SECTIONS -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_utils \ import NxField, get_memory_mapped_data diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_sections.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_sections.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_sections.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_sections.py index 737555975..26434a4ac 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_sections.py +++ b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_sections.py @@ -26,7 +26,7 @@ # from pint import UnitRegistry -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_apt6_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_apt6_utils \ import np_uint16_to_string, string_to_typed_nparray diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_sections_branches.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_sections_branches.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_sections_branches.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_sections_branches.py index 73aebdfcf..0067819af 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_sections_branches.py +++ b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_sections_branches.py @@ -22,7 +22,7 @@ # pylint: disable=E1101 -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_apt6_sections \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_apt6_sections \ import AptFileSectionMetadata diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_utils.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_utils.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_apt6_utils.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_apt6_utils.py diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_epos_reader.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_epos_reader.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_epos_reader.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_epos_reader.py index 8ce7d4dc2..11cb5fd68 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_epos_reader.py +++ b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_epos_reader.py @@ -26,7 +26,7 @@ import numpy as np -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_utils \ import NxField, get_memory_mapped_data diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_ods2metadata.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_ods2metadata.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_ods2metadata.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_ods2metadata.py diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_pos_reader.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_pos_reader.py similarity index 97% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_pos_reader.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_pos_reader.py index bb37b9377..825fbfb3b 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_pos_reader.py +++ b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_pos_reader.py @@ -26,7 +26,7 @@ import numpy as np -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_utils \ import NxField, get_memory_mapped_data diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_rng_reader.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_rng_reader.py similarity index 98% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_rng_reader.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_rng_reader.py index 9bbf426ce..a7f174021 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_rng_reader.py +++ b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_rng_reader.py @@ -25,7 +25,7 @@ import re import numpy as np -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_utils \ import NxField, NxIon, significant_range, create_isotope_vector, \ isotope_vector_to_dict_keyword diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_rrng_reader.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_rrng_reader.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_rrng_reader.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_rrng_reader.py index 1a7ef19f5..bbb2adc46 100644 --- a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_rrng_reader.py +++ b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_rrng_reader.py @@ -26,7 +26,7 @@ import numpy as np -from nexusparser.tools.dataconverter.readers.apm.utils.aptfim_io_utils \ +from nexusutils.dataconverter.readers.apm.utils.aptfim_io_utils \ import NxField, NxIon, significant_range, create_isotope_vector, \ isotope_vector_to_dict_keyword diff --git a/nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_utils.py b/nexusutils/dataconverter/readers/apm/utils/aptfim_io_utils.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/apm/utils/aptfim_io_utils.py rename to nexusutils/dataconverter/readers/apm/utils/aptfim_io_utils.py diff --git a/nexusutils/dataconverter/readers/base/README.md b/nexusutils/dataconverter/readers/base/README.md new file mode 100644 index 000000000..eb3bf3404 --- /dev/null +++ b/nexusutils/dataconverter/readers/base/README.md @@ -0,0 +1,4 @@ +# base reader + +## Contact person in FAIRmat for this reader +Sherjeel Shabih \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/base/__init__.py b/nexusutils/dataconverter/readers/base/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/base/__init__.py rename to nexusutils/dataconverter/readers/base/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/base/reader.py b/nexusutils/dataconverter/readers/base/reader.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/base/reader.py rename to nexusutils/dataconverter/readers/base/reader.py diff --git a/nexusutils/dataconverter/readers/ellips/README.md b/nexusutils/dataconverter/readers/ellips/README.md new file mode 100644 index 000000000..09e0eba92 --- /dev/null +++ b/nexusutils/dataconverter/readers/ellips/README.md @@ -0,0 +1,4 @@ +# ellips(ometry) reader + +## Contact person in FAIRmat for this reader +Carola Emminger \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/ellips/__init__.py b/nexusutils/dataconverter/readers/ellips/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/ellips/__init__.py rename to nexusutils/dataconverter/readers/ellips/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/ellips/reader.py b/nexusutils/dataconverter/readers/ellips/reader.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/ellips/reader.py rename to nexusutils/dataconverter/readers/ellips/reader.py index 7f6a7094d..e3192d3d8 100644 --- a/nexusparser/tools/dataconverter/readers/ellips/reader.py +++ b/nexusutils/dataconverter/readers/ellips/reader.py @@ -22,7 +22,7 @@ import pandas as pd import numpy as np # import h5py -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.readers.base.reader import BaseReader DEFAULT_HEADER = {'sep': '\t', 'skip': 0} diff --git a/nexusutils/dataconverter/readers/em_nion/README.md b/nexusutils/dataconverter/readers/em_nion/README.md new file mode 100644 index 000000000..6d2153837 --- /dev/null +++ b/nexusutils/dataconverter/readers/em_nion/README.md @@ -0,0 +1,12 @@ +# em_nion reader + +## Status +This reader is considered deprecated for two reasons: First, the NeXus application definition +NXem_nion has been superseeded by NXem, which is functionally and conceptually much more covering +and most importantly not restricted to users of Nion microscopes. Second, we have been working on an export +functionality inside nionswift. Nionswift is the control software for users of Nion microscopes. + +In effect, this reader will be removed with one of the next updates of nomad-parser-nexus. + +## Contact persons in FAIRmat for this reader and related functionality +Markus Kühbach and Sherjeel Shabih \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/em_nion/__init__.py b/nexusutils/dataconverter/readers/em_nion/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/em_nion/__init__.py rename to nexusutils/dataconverter/readers/em_nion/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/em_nion/reader.py b/nexusutils/dataconverter/readers/em_nion/reader.py similarity index 98% rename from nexusparser/tools/dataconverter/readers/em_nion/reader.py rename to nexusutils/dataconverter/readers/em_nion/reader.py index 111eafaba..dd301b09b 100644 --- a/nexusparser/tools/dataconverter/readers/em_nion/reader.py +++ b/nexusutils/dataconverter/readers/em_nion/reader.py @@ -30,12 +30,12 @@ import numpy as np -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.readers.base.reader import BaseReader -from nexusparser.tools.dataconverter.readers.em_nion.utils.em_io_utils_misc \ +from nexusutils.dataconverter.readers.em_nion.utils.em_io_utils_misc \ import recursive_query_nested_dict, assess_situation_with_input_files, NION_ERROR_CODES -from nexusparser.tools.dataconverter.readers.em_nion.utils.em_io_utils_ods2dct \ +from nexusutils.dataconverter.readers.em_nion.utils.em_io_utils_ods2dct \ import ods_to_json_routing_dict # each experiment on a given sample should be stored in an own file diff --git a/nexusparser/tools/dataconverter/readers/em_nion/utils/NionSwiftJsonToNexusTranslationTable.ods b/nexusutils/dataconverter/readers/em_nion/utils/NionSwiftJsonToNexusTranslationTable.ods similarity index 100% rename from nexusparser/tools/dataconverter/readers/em_nion/utils/NionSwiftJsonToNexusTranslationTable.ods rename to nexusutils/dataconverter/readers/em_nion/utils/NionSwiftJsonToNexusTranslationTable.ods diff --git a/nexusparser/tools/dataconverter/readers/em_nion/utils/em_io_utils_misc.py b/nexusutils/dataconverter/readers/em_nion/utils/em_io_utils_misc.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/em_nion/utils/em_io_utils_misc.py rename to nexusutils/dataconverter/readers/em_nion/utils/em_io_utils_misc.py diff --git a/nexusparser/tools/dataconverter/readers/em_nion/utils/em_io_utils_ods2dct.py b/nexusutils/dataconverter/readers/em_nion/utils/em_io_utils_ods2dct.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/em_nion/utils/em_io_utils_ods2dct.py rename to nexusutils/dataconverter/readers/em_nion/utils/em_io_utils_ods2dct.py diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/README.md b/nexusutils/dataconverter/readers/em_spctrscpy/README.md similarity index 73% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/README.md rename to nexusutils/dataconverter/readers/em_spctrscpy/README.md index 7be93a608..61f479841 100644 --- a/nexusparser/tools/dataconverter/readers/em_spctrscpy/README.md +++ b/nexusutils/dataconverter/readers/em_spctrscpy/README.md @@ -1,19 +1,22 @@ # em_spctrscpy reader ## Purpose -Translate diverse vendor and community file formats from atom probe microscopy into -a standardized representation using the NeXus application definition NXem. -This parser does not copy over all of the data and metadata in the vendor file(s) -but the particular subset which is understood and useful inside a NOMAD OASIS instance. +Translate diverse files from the scientific community and technology partners within +the electron microscopy community into a standardized representation using the NeXus +application definition NXem. +This parser does not copy over all of the data and metadata in files from especially +commercial software but that particular subset which is understood and useful +inside a NOMAD OASIS instance. ## What this em reader supports The main idea behind the parser is to offer users of the OASIS a diverse example of how a parser for specific file formats can be written and designed. We would like to encourage the EM community to share example files with us. These can be small and come from diverse use cases. -Ideally, these should represent data in vendor file formats other than the already supported ones, -so that we can broaden the applicability of this parser. +Ideally, these should represent data in file formats from technology partners other than the +already here supported and implemented ones. This would support us to broaden the applicability +of this parser. -Specifically, the implementation shows how I/O functionalities of hyperspy can be used +Specifically, the implementation shows how I/O functionalities of hyperspy can be used to load data of spectroscopy experiments from three exemplar file formats: Bruker BCF, Velox EMD, and DigitalMicrograph DM3. The implementation shows how instances of NeXus base classes like NXspectrum_set_em_xray, NXspectrum_set_em_eels, and NXimage_set_em_adf @@ -26,20 +29,20 @@ scanning electron microscopy (SEM) EDS/EDX, transmission electron microscopy ## Getting started - usage related to NOMAD OASIS This parser can be used to map numerical data and metadata inside frequently -used vendor file formats of electron microscopy software tools into a NeXus -HDF5 file which complies with a specific version of the NXem application +used file formats from technology partners of electron microscopy software tools +into a NeXus/HDF5 file which complies with a specific version of the NXem application definition. If you are using a NOMAD OASIS you can use this tool as follows. 1. Log-in to a NOMAD OASIS and navigate to the *Create Upload* tab. 2. Select EM example from the list of available options. -3. Drag-and-drop your files in vendor-specific formats, i.e. bcf, emd, dm3. +3. Drag-and-drop your files in specific file formats, i.e. bcf, emd, dm3. 3. Edit the electronic lab notebook (ELN) schema inside the NOMAD OASIS and click the save button in the NOMAD OASIS GUI to save the data that you have entered into the ELN template. Clicking *save* will trigger the automatic generation of an eln_data.yaml file. Second, the clicking will trigger a run of the dataconverter/em_spctrscpy parser which generates a NXem NeXus file based on the data - in the vendor file and the eln_data.yaml file. Afterwards, the file will be + file(s) from technology partners and the eln_data.yaml file. Afterwards, the file will be displayed in the GUI and upload section of your OASIS. By default the converter performs a strong loss-less compression on the input as many of the stack data store integers with a low entropy. @@ -51,17 +54,16 @@ If you are using a NOMAD OASIS you can use this tool as follows. its content with the H5Web tools inside the NOMAD OASIS GUI and click interactively through the data including default plots. For electron microscopy these are the EDS/EDX spectra stack, eventually an sum spectrum, annular dark field) overview images - of the material region-of-interest (ROI) characterized, and if present in the vendor - file composition maps. + of the material region-of-interest (ROI) characterized, and if present in composition maps. If unsuccessful, the data logger can help you to identify if problems occurred. Clearly as microscopy software tools differ, users should not expect that every required field in the application definition can be served by the data and metadata -from an arbitrary such microscopy tool and its often vendor-specific output (file -formats). Therefore, the em_spctrscpy reader takes the additional metadata from the -eln_data.yaml file. Specifically, this file can be created with the ELN schema creation -and customization functionalities offered through NOMAD OASIS or via any other ELN -or solution which can edit yaml files. +from an arbitrary such microscopy tool and its often specific formatting. Therefore, +the em_spctrscpy reader takes such additional metadata from the eln_data.yaml file. +Specifically, this file can be created with the ELN schema creation and customization +functionalities are offered through NOMAD OASIS or via any other ELN +or solution with which users can edit yaml files. ## Getting started - standalone usage If you use this dataconverter/em_spctrscpy parser as a standalone tool, @@ -87,7 +89,7 @@ for electron microscopy data inside NOMAD OASIS. ## Technical background details for developers and data scientists The em_spctrscpy reader serves as a parser with multiple parts/readers/and sub-parser components because data and metadata in electron microscopy come from such a diverse number of file -formats and use cases, from results of interactions with different GUIs, vendor scripts +formats and use cases, from results of interactions with different GUIs, scripts running inside GUIs, or user-customized/-written scripts using open-source microscopy software tools that it is essentially to keep things organized. These subtilities make the development of a general enough parser challenging. @@ -99,11 +101,13 @@ is breadth- rather than depth-first. Our approach is driven by examples. Breadth first means we would like to offer the user first an overview of the rather large number of NeXus base classes within the design of the NXem application definition. -Practically, the process needs to be driven by examples as many I/O routines of especially -vendor file formats in open-source software was designed by reverse engineering. In fact, -there is currently no joint knowledge base how all possible vendor files can be safely and -robustly parsed so that each field and entry is not only binarily readable but can also +Practically, the process needs to be driven by examples because many I/O routines for especially +file formats from technology partners inside open-source software was designed by reverse engineering. +Hyperspy is a good example of these developments and efforts. +In fact, there is currently no joint knowledge base how all possible file formats can be safely +and robustly parsed so that each field and entry is not only binarily readable but can also confidently be mapped on specific terms using a controlled vocabulary. +Interestingly this challenge is independent of the ontology used. Currently the example implements for: * NXspectrum_set_em_xray @@ -123,9 +127,8 @@ microscopy data. Our starting point in FAIRmat for EM was thus different compared to the situation in e.g. the field of atom probe microscopy. In the field of atom probe, only a few file formats exists and have been in use when the FAIRmat project started. -This is why dataconverter/apm has its own subroutines for loading intricate -details of vendor and open-source-documented file formats, which we have implemented -and offer as a reference implementation. +This is why dataconverter/em_spctrscpy has its own subroutines for loading intricate +details of files from the open-source community or technology partners. By contrast, for electron microscopy developing these many file format readers on our own is not a feasible approach for the FAIRmat project for two reasons: @@ -134,8 +137,8 @@ First, there is a very limited use of writing again readers for a specific EM fi because the EM community has developed already many of such a number of these by now. Many of them are mature in that they offer internal readers for several file formats. The strength of the existent readers is that many users already work with such software. -Thus, supporting the development and working together on I/O functions for vendor files -and discussing open issues is in our opinion the preferred approach. +Thus, supporting the development and working together on I/O functions for files +from technology partners and discussing open issues is in our opinion the preferred approach. Specific examples of such community tools are: **hyperspy** for analyses of spectra such as EDX/EDS and EELS, used in SEM/TEM communities @@ -149,32 +152,29 @@ should be used by even more people to support the respective open-source project The other reason why we are not convinced that it is a sustainable approach for a National Research Data Infrastructure that each project implements own formats is that there are already two important challenges with the current status quo in electron microscopy: -Format constraints and limited documentation of the content and details behind -some of the vendor file formats. We should make clear that we acknowledge the -significant momentum and effort which is ongoing at microscopy manufacturing companies -on implementing strategies for their software tools to store and document metadata. -We would like to see though that more of these efforts become documented in the literature -and the public domain. - -## A request to take action by the vendors -While vendor software is used by numerous of microscopists every day it is interesting to note +Format constraints and limited documentation of the content and details behind +some of the file formats from technology partners. We should make clear that we acknowledge +the significant momentum and effort microscopy manufacturers as technology partners invest +into the storing of metadata in their (commercial) software solutions. +We would like to see though that more of these efforts become documented in the +literature and the public domain. + +## A request to take action by technology partners and the scientific community +While commercial software is used by numerous microscopists every day it is interesting to note that the detailed knowledge about the I/O routines has always been on a few developers shoulders. We have realized that many of the file format readers in open-source software were reverse-engineered. This is challenging because the amount of documentation that is available -especially for some vendor file formats is neither exhaustive nor detailed enough. +especially for some file formats is neither exhaustive nor documented in detail enough. This limits developers when they have to decide and design how to best implement the mapping of specific binary numerical data and metadata into specifically named fields. -Here we hope that intensified exchange between vendors and the community can help to -improve the situation. You are very welcome to leave us comments in the issue list to -exchange specifically about this topic. Even better would be if commercial software tools -evolve into a state that they offer complementary options for exporting detailed metadata -and numerical data through publicly documented formats. +Here we hope that intensified exchange between technology partners and the scientific community +can help to improve the situation. -In fact, limited technical documentation of some vendor file formats stands in strong -contrast to the powerful GUI-based tools and the in fact continuous efforts of the vendors -to make the barriers for working with microscopy data simpler and become more aligned with the -FAIR principles. +You are very welcome to leave us comments in the issue list (or drop us an email) to exchange +specifically about this topic. Even better would be if commercial software tools evolve +into a state that they offer complementary options for exporting detailed metadata +and numerical data through publicly documented formats. ## A starting point to harmonize metadata and numerical data from scripting based solutions It is noteworthy that internally many of tools, whether it be commercial or open source tools, @@ -184,3 +184,6 @@ Therefore, even though users of tools like mtex or hyperspy may in practice crea different scripts, they still interact with a restricted set of class instances and methods. In effect, having these classes offers a possibility for developing more generic parsers like what is here exemplified with the dataconverter/em_spctrscpy parser. + +## Contact person in FAIRmat for this reader +Markus Kühbach \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/__init__.py b/nexusutils/dataconverter/readers/em_spctrscpy/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/__init__.py rename to nexusutils/dataconverter/readers/em_spctrscpy/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/reader.py b/nexusutils/dataconverter/readers/em_spctrscpy/reader.py similarity index 94% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/reader.py rename to nexusutils/dataconverter/readers/em_spctrscpy/reader.py index 305680345..2ad1e4672 100644 --- a/nexusparser/tools/dataconverter/readers/em_spctrscpy/reader.py +++ b/nexusutils/dataconverter/readers/em_spctrscpy/reader.py @@ -30,27 +30,27 @@ import hyperspy.api as hs -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.readers.base.reader import BaseReader -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.em_use_case_selector \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.em_use_case_selector \ import EmUseCaseSelector -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.em_nexus_base_classes \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.em_nexus_base_classes \ import NxObject -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.em_nomad_oasis_eln \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.em_nomad_oasis_eln \ import NxEmNomadOasisElnSchemaParser -# from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.oina.em_oina_xray \ +# from nexusutils.dataconverter.readers.em_spctrscpy.utils.oina.em_oina_xray \ # import NxOinaSpectrumSetEmXray -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.hspy.em_hspy_xray \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.hspy.em_hspy_xray \ import NxSpectrumSetEmXray -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.hspy.em_hspy_eels \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.hspy.em_hspy_eels \ import NxSpectrumSetEmEels -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.hspy.em_hspy_adf \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.hspy.em_hspy_adf \ import NxImageSetEmAdf diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_nexus_base_classes.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/em_nexus_base_classes.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_nexus_base_classes.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/em_nexus_base_classes.py index c2cd7848e..2aac71015 100644 --- a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_nexus_base_classes.py +++ b/nexusutils/dataconverter/readers/em_spctrscpy/utils/em_nexus_base_classes.py @@ -24,7 +24,7 @@ from typing import Dict -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.em_versioning \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.em_versioning \ import NX_EM_ADEF_NAME, NX_EM_ADEF_VERSION, \ NX_EM_EXEC_NAME, NX_EM_EXEC_VERSION diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_nomad_oasis_eln.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/em_nomad_oasis_eln.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_nomad_oasis_eln.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/em_nomad_oasis_eln.py index 3a4757670..b52a82bc5 100644 --- a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_nomad_oasis_eln.py +++ b/nexusutils/dataconverter/readers/em_spctrscpy/utils/em_nomad_oasis_eln.py @@ -30,7 +30,7 @@ from ase.data import chemical_symbols -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.em_versioning \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.em_versioning \ import NX_EM_ADEF_NAME, NX_EM_ADEF_VERSION, NX_EM_EXEC_NAME, NX_EM_EXEC_VERSION diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_use_case_selector.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/em_use_case_selector.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_use_case_selector.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/em_use_case_selector.py diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_versioning.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/em_versioning.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/em_versioning.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/em_versioning.py diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_adf.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_adf.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_adf.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_adf.py index 10c5bc007..e2bd0b8f9 100644 --- a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_adf.py +++ b/nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_adf.py @@ -28,7 +28,7 @@ import hyperspy.api as hs -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.em_nexus_base_classes \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.em_nexus_base_classes \ import NxObject diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_comments.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_comments.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_comments.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_comments.py diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_eels.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_eels.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_eels.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_eels.py index 89e45975a..655f31b68 100644 --- a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_eels.py +++ b/nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_eels.py @@ -28,7 +28,7 @@ import hyperspy.api as hs -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.em_nexus_base_classes \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.em_nexus_base_classes \ import NxObject diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_xray.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_xray.py similarity index 99% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_xray.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_xray.py index 3652f36b4..7e189afda 100644 --- a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_xray.py +++ b/nexusutils/dataconverter/readers/em_spctrscpy/utils/hspy/em_hspy_xray.py @@ -28,7 +28,7 @@ import hyperspy.api as hs -from nexusparser.tools.dataconverter.readers.em_spctrscpy.utils.em_nexus_base_classes \ +from nexusutils.dataconverter.readers.em_spctrscpy.utils.em_nexus_base_classes \ import NxObject diff --git a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/oina/em_oina_xray.py b/nexusutils/dataconverter/readers/em_spctrscpy/utils/oina/em_oina_xray.py similarity index 91% rename from nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/oina/em_oina_xray.py rename to nexusutils/dataconverter/readers/em_spctrscpy/utils/oina/em_oina_xray.py index 8d4e15a9f..d514a0b8d 100644 --- a/nexusparser/tools/dataconverter/readers/em_spctrscpy/utils/oina/em_oina_xray.py +++ b/nexusutils/dataconverter/readers/em_spctrscpy/utils/oina/em_oina_xray.py @@ -26,5 +26,5 @@ # import numpy as np -# from nexusparser.tools.dataconverter.readers.em.utils.em_nexus_base_classes \ +# from nexusutils.dataconverter.readers.em.utils.em_nexus_base_classes \ # import NxObject diff --git a/nexusutils/dataconverter/readers/example/README.md b/nexusutils/dataconverter/readers/example/README.md new file mode 100644 index 000000000..e188717b1 --- /dev/null +++ b/nexusutils/dataconverter/readers/example/README.md @@ -0,0 +1,5 @@ +# example reader + +## Contact person in FAIRmat for this reader +Sherjeel Shabih +Andrea Albino \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/example/__init__.py b/nexusutils/dataconverter/readers/example/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/example/__init__.py rename to nexusutils/dataconverter/readers/example/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/example/reader.py b/nexusutils/dataconverter/readers/example/reader.py similarity index 94% rename from nexusparser/tools/dataconverter/readers/example/reader.py rename to nexusutils/dataconverter/readers/example/reader.py index d12284ab6..3d33c72a8 100644 --- a/nexusparser/tools/dataconverter/readers/example/reader.py +++ b/nexusutils/dataconverter/readers/example/reader.py @@ -14,6 +14,7 @@ # 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. + # """An example reader implementation for the DataConverter.""" import os @@ -21,7 +22,7 @@ import json import numpy as np -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.readers.base.reader import BaseReader class ExampleReader(BaseReader): @@ -74,14 +75,14 @@ def read(self, template[("/ENTRY" "[entry]/test_link" "/external_link")] = {"link": - f"{os.path.dirname(__file__)}/../../../../../tests/" - f"data/tools/dataconverter/readers/mpes/" + f"{os.path.dirname(__file__)}/../../../../tests/" + f"data/dataconverter/readers/mpes/" f"xarray_saved_small_calibration.h5:/axes/ax3" } # virtual datasets concatenation - my_path = str(f"{os.path.dirname(__file__)}/../../../../../tests/" - f"data/tools/dataconverter/readers/mpes") + my_path = str(f"{os.path.dirname(__file__)}/../../../../tests/" + f"data/dataconverter/readers/mpes") my_datasets = {"link": [f"{my_path}/xarray_saved_small_calibration.h5:/axes/ax0", f"{my_path}/xarray_saved_small_calibration.h5:/axes/ax1", @@ -91,8 +92,8 @@ def read(self, template["/ENTRY[entry]/test_virtual_dataset/concatenate_datasets"] = my_datasets # virtual datasets slicing - my_path = str(f"{os.path.dirname(__file__)}/../../../../../tests/" - f"data/tools/dataconverter/readers/mpes") + my_path = str(f"{os.path.dirname(__file__)}/../../../../tests/" + f"data/dataconverter/readers/mpes") template[("/ENTRY[entry]" "/test_virtual" "_dataset/sliced" diff --git a/nexusutils/dataconverter/readers/hall/README.md b/nexusutils/dataconverter/readers/hall/README.md new file mode 100644 index 000000000..4c39ca3a0 --- /dev/null +++ b/nexusutils/dataconverter/readers/hall/README.md @@ -0,0 +1,4 @@ +# hall reader + +## Contact person in FAIRmat for this reader +Florian Dobner \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/hall/__init__.py b/nexusutils/dataconverter/readers/hall/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/hall/__init__.py rename to nexusutils/dataconverter/readers/hall/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/hall/helpers.py b/nexusutils/dataconverter/readers/hall/helpers.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/hall/helpers.py rename to nexusutils/dataconverter/readers/hall/helpers.py diff --git a/nexusparser/tools/dataconverter/readers/hall/reader.py b/nexusutils/dataconverter/readers/hall/reader.py similarity index 95% rename from nexusparser/tools/dataconverter/readers/hall/reader.py rename to nexusutils/dataconverter/readers/hall/reader.py index de72d8a6a..4f2a57787 100644 --- a/nexusparser/tools/dataconverter/readers/hall/reader.py +++ b/nexusutils/dataconverter/readers/hall/reader.py @@ -21,9 +21,9 @@ import numpy as np import pandas as pd -from nexusparser.tools.dataconverter.readers.json_yml.reader import YamlJsonReader -import nexusparser.tools.dataconverter.readers.hall.helpers as helpers -from nexusparser.tools.dataconverter.readers.utils import parse_json, parse_yml +from nexusutils.dataconverter.readers.json_yml.reader import YamlJsonReader +import nexusutils.dataconverter.readers.hall.helpers as helpers +from nexusutils.dataconverter.readers.utils import parse_json, parse_yml # Replacement dict for section names SECTION_REPLACEMENTS = { diff --git a/nexusparser/tools/dataconverter/readers/json_map/Readme.md b/nexusutils/dataconverter/readers/json_map/README.md similarity index 92% rename from nexusparser/tools/dataconverter/readers/json_map/Readme.md rename to nexusutils/dataconverter/readers/json_map/README.md index 6fa0de5c0..4b4820c49 100644 --- a/nexusparser/tools/dataconverter/readers/json_map/Readme.md +++ b/nexusutils/dataconverter/readers/json_map/README.md @@ -18,4 +18,7 @@ There are some example files you can use: ```console user@box:~$ python convert.py --nxdl NXtest --input-file data.json --input-file data.mapping.json --reader json_map -``` \ No newline at end of file +``` + +## Contact person in FAIRmat for this reader +Sherjeel Shabih \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/json_map/__init__.py b/nexusutils/dataconverter/readers/json_map/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/json_map/__init__.py rename to nexusutils/dataconverter/readers/json_map/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/json_map/reader.py b/nexusutils/dataconverter/readers/json_map/reader.py similarity index 96% rename from nexusparser/tools/dataconverter/readers/json_map/reader.py rename to nexusutils/dataconverter/readers/json_map/reader.py index fa64571de..9d42516e7 100644 --- a/nexusparser/tools/dataconverter/readers/json_map/reader.py +++ b/nexusutils/dataconverter/readers/json_map/reader.py @@ -22,9 +22,9 @@ import numpy as np import xarray -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader -from nexusparser.tools.dataconverter.template import Template -from nexusparser.tools.dataconverter.helpers import ensure_all_required_fields_exist +from nexusutils.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.template import Template +from nexusutils.dataconverter.helpers import ensure_all_required_fields_exist def parse_slice(slice_string): diff --git a/nexusutils/dataconverter/readers/json_yml/README.md b/nexusutils/dataconverter/readers/json_yml/README.md new file mode 100644 index 000000000..eb6ed4eef --- /dev/null +++ b/nexusutils/dataconverter/readers/json_yml/README.md @@ -0,0 +1,4 @@ +# JSON YAML reader + +## Contact person in FAIRmat for this reader +Sherjeel Shabih \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/json_yml/__init__.py b/nexusutils/dataconverter/readers/json_yml/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/json_yml/__init__.py rename to nexusutils/dataconverter/readers/json_yml/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/json_yml/reader.py b/nexusutils/dataconverter/readers/json_yml/reader.py similarity index 96% rename from nexusparser/tools/dataconverter/readers/json_yml/reader.py rename to nexusutils/dataconverter/readers/json_yml/reader.py index 707b51a8a..099aac401 100644 --- a/nexusparser/tools/dataconverter/readers/json_yml/reader.py +++ b/nexusutils/dataconverter/readers/json_yml/reader.py @@ -19,7 +19,7 @@ from typing import Tuple, Any, Callable, Dict, List import os -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.readers.base.reader import BaseReader class YamlJsonReader(BaseReader): diff --git a/nexusutils/dataconverter/readers/mpes/README.md b/nexusutils/dataconverter/readers/mpes/README.md new file mode 100644 index 000000000..c189d6a47 --- /dev/null +++ b/nexusutils/dataconverter/readers/mpes/README.md @@ -0,0 +1,4 @@ +# mpes reader + +## Contact person in FAIRmat for this reader +Florian Dobner diff --git a/nexusparser/tools/dataconverter/readers/mpes/__init__.py b/nexusutils/dataconverter/readers/mpes/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/mpes/__init__.py rename to nexusutils/dataconverter/readers/mpes/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/mpes/reader.py b/nexusutils/dataconverter/readers/mpes/reader.py similarity index 98% rename from nexusparser/tools/dataconverter/readers/mpes/reader.py rename to nexusutils/dataconverter/readers/mpes/reader.py index d004fcbb3..723f8dc41 100644 --- a/nexusparser/tools/dataconverter/readers/mpes/reader.py +++ b/nexusutils/dataconverter/readers/mpes/reader.py @@ -27,8 +27,8 @@ import xarray as xr import yaml -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader -from nexusparser.tools.dataconverter.readers.utils import flatten_and_replace +from nexusutils.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.readers.utils import flatten_and_replace DEFAULT_UNITS = { "X": "step", diff --git a/nexusutils/dataconverter/readers/transmission/README.md b/nexusutils/dataconverter/readers/transmission/README.md new file mode 100644 index 000000000..0fd071f32 --- /dev/null +++ b/nexusutils/dataconverter/readers/transmission/README.md @@ -0,0 +1,4 @@ +# transmission reader + +## Contact person in FAIRmat for this reader +The FAIRmat Area B team \ No newline at end of file diff --git a/nexusparser/tools/dataconverter/readers/transmission/__init__.py b/nexusutils/dataconverter/readers/transmission/__init__.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/transmission/__init__.py rename to nexusutils/dataconverter/readers/transmission/__init__.py diff --git a/nexusparser/tools/dataconverter/readers/transmission/metadata_parsers.py b/nexusutils/dataconverter/readers/transmission/metadata_parsers.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/transmission/metadata_parsers.py rename to nexusutils/dataconverter/readers/transmission/metadata_parsers.py diff --git a/nexusparser/tools/dataconverter/readers/transmission/reader.py b/nexusutils/dataconverter/readers/transmission/reader.py similarity index 97% rename from nexusparser/tools/dataconverter/readers/transmission/reader.py rename to nexusutils/dataconverter/readers/transmission/reader.py index ac1622b44..919dc4bb7 100644 --- a/nexusparser/tools/dataconverter/readers/transmission/reader.py +++ b/nexusutils/dataconverter/readers/transmission/reader.py @@ -20,9 +20,9 @@ from typing import Callable, List, Any, Dict import pandas as pd -from nexusparser.tools.dataconverter.readers.json_yml.reader import YamlJsonReader -import nexusparser.tools.dataconverter.readers.transmission.metadata_parsers as mpars -from nexusparser.tools.dataconverter.readers.utils import parse_json, parse_yml +from nexusutils.dataconverter.readers.json_yml.reader import YamlJsonReader +import nexusutils.dataconverter.readers.transmission.metadata_parsers as mpars +from nexusutils.dataconverter.readers.utils import parse_json, parse_yml # Dictionary mapping metadata in the asc file to the paths in the NeXus file. diff --git a/nexusparser/tools/dataconverter/readers/utils.py b/nexusutils/dataconverter/readers/utils.py similarity index 100% rename from nexusparser/tools/dataconverter/readers/utils.py rename to nexusutils/dataconverter/readers/utils.py diff --git a/nexusparser/tools/dataconverter/template.py b/nexusutils/dataconverter/template.py similarity index 99% rename from nexusparser/tools/dataconverter/template.py rename to nexusutils/dataconverter/template.py index 7a02f324f..143b03e45 100644 --- a/nexusparser/tools/dataconverter/template.py +++ b/nexusutils/dataconverter/template.py @@ -20,7 +20,7 @@ import copy import json -from nexusparser.tools.dataconverter import helpers +from nexusutils.dataconverter import helpers class Template(dict): diff --git a/nexusparser/tools/dataconverter/writer.py b/nexusutils/dataconverter/writer.py similarity index 96% rename from nexusparser/tools/dataconverter/writer.py rename to nexusutils/dataconverter/writer.py index 3552f544e..a09b51238 100644 --- a/nexusparser/tools/dataconverter/writer.py +++ b/nexusutils/dataconverter/writer.py @@ -15,7 +15,7 @@ # See the License for the specific language governing permissions and # limitations under the License. # -"""The writer class for writing a Nexus file in accordance with a given NXDL.""" +"""The writer class for writing a NeXus file in accordance with a given NXDL.""" import copy import logging @@ -25,8 +25,8 @@ import h5py import numpy as np -from nexusparser.tools.dataconverter import helpers -from nexusparser.tools import nexus +from nexusutils.dataconverter import helpers +from nexusutils.nexus import nexus logger = logging.getLogger(__name__) # pylint: disable=C0103 logger.setLevel(logging.INFO) @@ -160,17 +160,17 @@ def handle_dicts_entries(data, grp, entry_name, output_path): class Writer: - """The writer class for writing a Nexus file in accordance with a given NXDL. + """The writer class for writing a NeXus file in accordance with a given NXDL. Args: data (dict): Dictionary containing the data to convert. nxdl_path (str): Path to the nxdl file to use during conversion. - output_path (str): Path to the output Nexus file. + output_path (str): Path to the output NeXus file. Attributes: data (dict): Dictionary containing the data to convert. nxdl_path (str): Path to the nxdl file to use during conversion. - output_path (str): Path to the output Nexus file. + output_path (str): Path to the output NeXus file. output_nexus (h5py.File): The h5py file object to manipulate output file. nxdl_data (dict): Stores xml data from given nxdl file to use during conversion. nxs_namespace (str): The namespace used in the NXDL tags. Helps search for XML children. @@ -222,7 +222,7 @@ def ensure_and_get_parent_node(self, path: str, undocumented_paths) -> h5py.Grou return self.output_nexus[parent_path_hdf5] def write(self): - """Writes the Nexus file with previously validated data from the reader with NXDL attrs.""" + """Writes the NeXus file with previously validated data from the reader with NXDL attrs.""" hdf5_links_for_later = [] for path, value in self.data.items(): diff --git a/nexusparser/definitions b/nexusutils/definitions similarity index 100% rename from nexusparser/definitions rename to nexusutils/definitions diff --git a/nexusutils/nexus/README.md b/nexusutils/nexus/README.md new file mode 100644 index 000000000..6d45bb380 --- /dev/null +++ b/nexusutils/nexus/README.md @@ -0,0 +1,12 @@ +The **nexus.py** tool can be used as a standalone tool **Testing nexus*** + +Following example dataset can be used to test `nexus.py` module `tests/data/nexus/201805_WSe2_arpes.nxs`. +This is an angular-resolved photoelectron spectroscopy (ARPES) dataset and it is formatted according to +the [NXarpes application definition of NEXUS](https://manual.nexusformat.org/classes/applications/NXarpes.html#nxarpes). + +Run the following command to test the `nexus.py` using example ARPES dataset: +``` +python test_parser.py +``` + +You should get a message reading "Testing of nexus.py is SUCCESSFUL." if everything goes as expected! diff --git a/nexusparser/metainfo/__init__.py b/nexusutils/nexus/__init__.py similarity index 88% rename from nexusparser/metainfo/__init__.py rename to nexusutils/nexus/__init__.py index 83ea3639f..2290aef3b 100644 --- a/nexusparser/metainfo/__init__.py +++ b/nexusutils/nexus/__init__.py @@ -4,8 +4,7 @@ # # Copyright The NOMAD Authors. # -# This file is part of NOMAD. -# See https://nomad-lab.eu for further info. +# 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. diff --git a/nexusparser/tools/nexus.py b/nexusutils/nexus/nexus.py similarity index 98% rename from nexusparser/tools/nexus.py rename to nexusutils/nexus/nexus.py index 5181ba6c3..62cb91d14 100644 --- a/nexusparser/tools/nexus.py +++ b/nexusutils/nexus/nexus.py @@ -1,5 +1,5 @@ # pylint: disable=too-many-lines -"""Read files from different format and print it in a standard Nexus format +"""Read files from different format and print it in a standard NeXus format """ import os @@ -99,7 +99,7 @@ def get_nx_namefit(hdf_name, name): def get_nx_classes(): - """Read base classes from the Nexus definition folder. + """Read base classes from the NeXus definition folder. Check each file in base_classes, applications, contributed_definitions. If its category attribute is 'base', then it is added to the list. """ base_classes = glob(os.path.join(get_nexus_definitions_path(), @@ -119,7 +119,7 @@ def get_nx_classes(): def get_nx_units(): - """Read unit kinds from the Nexus definition/nxdlTypes.xsd file""" + """Read unit kinds from the NeXus definition/nxdlTypes.xsd file""" filepath = f"{get_nexus_definitions_path()}{os.sep}nxdlTypes.xsd" tree = ET.parse(filepath) root = tree.getroot() @@ -142,7 +142,7 @@ def get_nx_units(): def get_nx_attribute_type(): - """Read attribute types from the Nexus definition/nxdlTypes.xsd file""" + """Read attribute types from the NeXus definition/nxdlTypes.xsd file""" filepath = get_nexus_definitions_path() + '/nxdlTypes.xsd' tree = ET.parse(filepath) root = tree.getroot() @@ -786,7 +786,7 @@ def get_node_at_nxdl_path(nxdl_path: str = None, nx_name: str = None, elem: ET.Element = None, exc: bool = True): """Returns an ET.Element for the given path. - This function either takes the name for the Nexus Application Definition + This function either takes the name for the NeXus Application Definition we are looking for or the root elem from a previously loaded NXDL file and finds the corresponding XML element with the needed attributes.""" (class_path, nxdlpath, elist) = get_inherited_nodes(nxdl_path, nx_name, elem) @@ -1033,8 +1033,9 @@ class HandleNexus: """documentation""" def __init__(self, logger, args): self.logger = logger + local_dir = os.path.abspath(os.path.dirname(__file__)) self.input_file_name = args[0] if len( - args) >= 1 else 'tests/data/nexus_test_data/201805_WSe2_arpes.nxs' + args) >= 1 else os.path.join(local_dir, '../../tests/data/nexus/201805_WSe2_arpes.nxs') self.parser = None self.in_file = None @@ -1058,8 +1059,10 @@ def main(): logging_format = "%(levelname)s: %(message)s" stdout_handler = logging.StreamHandler(sys.stdout) stdout_handler.setLevel(logging.DEBUG) - logging.basicConfig(level=logging.DEBUG, format=logging_format, handlers=[stdout_handler]) - logger = logging.getLogger() + logging.basicConfig(level=logging.INFO, format=logging_format, handlers=[stdout_handler]) + logger = logging.getLogger(__name__) + logger.addHandler(stdout_handler) + logger.setLevel(logging.DEBUG) nexus_helper = HandleNexus(logger, sys.argv[1:]) nexus_helper.process_nexus_master_file(None) diff --git a/nexusparser/tools/yaml2nxdl/README.md b/nexusutils/nyaml2nxdl/README.md similarity index 75% rename from nexusparser/tools/yaml2nxdl/README.md rename to nexusutils/nyaml2nxdl/README.md index b1e93cad8..b720a1727 100644 --- a/nexusparser/tools/yaml2nxdl/README.md +++ b/nexusutils/nyaml2nxdl/README.md @@ -1,7 +1,8 @@ # YAML to NXDL converter and NXDL to YAML converter -**Tools purpose**: Offer a simple YAML-based schema and a XML-based schema to describe NeXus instances. These can be NeXus application definitions, or classes such as base or contributed classes. Users either create NeXus instances by writing a YAML file or a XML file which details a hierarchy of data/metadata elements. -The forward (YAML -> XML) and backward (XML -> YAML) conversions are implemented. +**Tools purpose**: Offer a simple YAML-based schema and a XML-based schema to describe NeXus instances. These can be NeXus application definitions or classes +such as base or contributed classes. Users either create NeXus instances by writing a YAML file or a XML file which details a hierarchy of data/metadata elements. +The forward (YAML -> NXDL.XML) and backward (NXDL.XML -> YAML) conversions are implemented. **How the tool works**: - yaml2nxdl.py @@ -11,8 +12,8 @@ The forward (YAML -> XML) and backward (XML -> YAML) conversions are implemented 3. Write the tree into a YAML file or a properly formatted NXDL XML schema file to disk. 4. Optionally, if --append argument is given, the XML or YAML input file is interpreted as an extension of a base class and the entries contained in it - are appended below a standard Nexus base class. - You need to specify both your input file (with YAML or XML extension) and Nexus class (with no extension). + are appended below a standard NeXus base class. + You need to specify both your input file (with YAML or XML extension) and NeXus class (with no extension). Both .yml and .nxdl.xml file of the extended class are printed. ```console @@ -29,6 +30,8 @@ Options: ``` +## Documentation + **Rule set**: From transcoding YAML files we need to follow several rules. * Named NeXus groups, which are instances of NeXus classes especially base or contributed classes. Creating (NXbeam) is a simple example of a request to define a group named according to NeXus default rules. mybeam1(NXbeam) or mybeam2(NXbeam) are examples how to create multiple named instances at the same hierarchy level. * Members of groups so-called fields. A simple example of a member is voltage. Here the datatype is implied automatically as the default NeXus NX_CHAR type. By contrast, voltage(NX_FLOAT) can be used to instantiate a member of class which should be of NeXus type NX_FLOAT. @@ -41,3 +44,12 @@ Options: * *units* A statement introducing NeXus-compliant NXDL units arguments, like NX_VOLTAGE * *dimensions* Details which dimensional arrays to expect * *enumeration* Python list of strings which are considered as recommended entries to choose from. + +## Next steps + +The NOMAD team is currently working on the establishing of a one-to-one mapping between +NeXus definitions and the NOMAD MetaInfo. As soon as this is in place the YAML files will +be annotated with further metadata so that they can serve two purposes. +On the one hand they can serve as an instance for a schema to create a GUI representation +of a NOMAD Oasis ELN schema. On the other hand the YAML to NXDL converter will skip all +those pieces of information which are irrelevant from a NeXus perspective. diff --git a/nexusparser/tools/yaml2nxdl/__init__.py b/nexusutils/nyaml2nxdl/__init__.py similarity index 100% rename from nexusparser/tools/yaml2nxdl/__init__.py rename to nexusutils/nyaml2nxdl/__init__.py diff --git a/nexusparser/tools/yaml2nxdl/yaml2nxdl.py b/nexusutils/nyaml2nxdl/nyaml2nxdl.py similarity index 90% rename from nexusparser/tools/yaml2nxdl/yaml2nxdl.py rename to nexusutils/nyaml2nxdl/nyaml2nxdl.py index 681d5fa1e..165e4bc4e 100755 --- a/nexusparser/tools/yaml2nxdl/yaml2nxdl.py +++ b/nexusutils/nyaml2nxdl/nyaml2nxdl.py @@ -35,8 +35,8 @@ import click from ..dataconverter import helpers -from . import yaml2nxdl_forward_tools -from . import yaml2nxdl_backward_tools +from . import nyaml2nxdl_forward_tools +from . import nyaml2nxdl_backward_tools def pretty_print_xml(xml_root, output_xml): @@ -73,13 +73,13 @@ def pretty_print_xml(xml_root, output_xml): os.remove('tmp.xml') -def yaml2nxdl(input_file: str, verbose: bool): - """Main of the yaml2nxdl converter, creates XML tree, +def nyaml2nxdl(input_file: str, verbose: bool): + """Main of the nyaml2nxdl converter, creates XML tree, namespace and schema, then evaluates a dictionary nest of groups recursively and fields or (their) attributes as childs of the groups """ - yml_appdef = yaml2nxdl_forward_tools.yml_reader(input_file) + yml_appdef = nyaml2nxdl_forward_tools.yml_reader(input_file) if verbose: sys.stdout.write(f'input-file: {input_file}\n') @@ -107,17 +107,17 @@ def yaml2nxdl(input_file: str, verbose: bool): del yml_appdef['category'] if 'symbols' in yml_appdef.keys(): - yaml2nxdl_forward_tools.xml_handle_symbols(yml_appdef, - xml_root, - 'symbols', - yml_appdef['symbols']) + nyaml2nxdl_forward_tools.xml_handle_symbols(yml_appdef, + xml_root, + 'symbols', + yml_appdef['symbols']) del yml_appdef['symbols'] assert isinstance(yml_appdef['doc'], str) and yml_appdef['doc'] != '', 'Doc \ has to be a non-empty string!' doctag = ET.SubElement(xml_root, 'doc') - doctag.text = yaml2nxdl_forward_tools.format_nxdl_doc(yml_appdef['doc']) + doctag.text = nyaml2nxdl_forward_tools.format_nxdl_doc(yml_appdef['doc']) del yml_appdef['doc'] @@ -143,7 +143,7 @@ def yaml2nxdl(input_file: str, verbose: bool): assert (keyword[0:2] == 'NX' and len(keyword) > 2), 'NX \ keyword has an invalid pattern, or is too short!' - yaml2nxdl_forward_tools.recursive_build(xml_root, yml_appdef[keyword], verbose) + nyaml2nxdl_forward_tools.recursive_build(xml_root, yml_appdef[keyword], verbose) pretty_print_xml(xml_root, input_file.rsplit(".", 1)[0] + '.nxdl.xml') if verbose: @@ -326,7 +326,7 @@ def xmlparse(self, output_yml, xml_tree, depth, verbose): parent = get_node_parent_info(tree, node)[0] doc_parent = helpers.remove_namespace_from_tag(parent.tag) if doc_parent != 'item': - yaml2nxdl_backward_tools.handle_not_root_level_doc(depth, node, file_out) + nyaml2nxdl_backward_tools.handle_not_root_level_doc(depth, node, file_out) if tag == ('symbols'): Nxdl2yaml.handle_symbols(self, depth, node) self.jump_symbol_child = True @@ -339,13 +339,13 @@ def xmlparse(self, output_yml, xml_tree, depth, verbose): Nxdl2yaml.print_root_level_info(self, depth, file_out) # End of print root-level definitions in file if tag in ('field', 'group') and depth != 0: - yaml2nxdl_backward_tools.handle_group_or_field(depth, node, file_out) + nyaml2nxdl_backward_tools.handle_group_or_field(depth, node, file_out) if tag == ('enumeration'): - yaml2nxdl_backward_tools.handle_enumeration(depth, node, file_out) + nyaml2nxdl_backward_tools.handle_enumeration(depth, node, file_out) if tag == ('attribute'): - yaml2nxdl_backward_tools.handle_attributes(depth, node, file_out) + nyaml2nxdl_backward_tools.handle_attributes(depth, node, file_out) if tag == ('dimensions'): - yaml2nxdl_backward_tools.handle_dimension(depth, node, file_out) + nyaml2nxdl_backward_tools.handle_dimension(depth, node, file_out) depth += 1 # Write nested nodes Nxdl2yaml.recursion_in_xml_tree(self, depth, xml_tree, output_yml, verbose) @@ -366,20 +366,20 @@ def print_yml(input_file, verbose): def append_yml(input_file, append, verbose): - """Append to an existing Nexus base class new elements provided in YML input file \ + """Append to an existing NeXus base class new elements provided in YML input file \ and print both an XML and YML file of the extended base class. """ nexus_def_path = os.path.join(os.path.abspath(os.path.dirname(__file__)), '../../definitions') assert [s for s in os.listdir(os.path.join(nexus_def_path, 'base_classes') ) if append.strip() == s.replace('.nxdl.xml', '')], \ - 'Your base class extension does not match any existing Nexus base classes' + 'Your base class extension does not match any existing NeXus base classes' tree = ET.parse(os.path.join(nexus_def_path + '/base_classes', append + '.nxdl.xml')) root = tree.getroot() # warning: tmp files are printed on disk and removed at the ends!! pretty_print_xml(root, 'tmp.nxdl.xml') print_yml('tmp.nxdl.xml', verbose) - yaml2nxdl('tmp_parsed.yml', verbose) + nyaml2nxdl('tmp_parsed.yml', verbose) tree = ET.parse('tmp_parsed.nxdl.xml') tree2 = ET.parse(input_file) root_no_duplicates = ET.Element( @@ -398,21 +398,21 @@ def append_yml(input_file, append, verbose): root_doc.text = elems.text break group = '{http://definition.nexusformat.org/nxdl/3.1}group' - root_no_duplicates = yaml2nxdl_backward_tools.compare_niac_and_my(tree, tree2, verbose, - group, - root_no_duplicates) + root_no_duplicates = nyaml2nxdl_backward_tools.compare_niac_and_my(tree, tree2, verbose, + group, + root_no_duplicates) field = '{http://definition.nexusformat.org/nxdl/3.1}field' - root_no_duplicates = yaml2nxdl_backward_tools.compare_niac_and_my(tree, tree2, verbose, - field, - root_no_duplicates) + root_no_duplicates = nyaml2nxdl_backward_tools.compare_niac_and_my(tree, tree2, verbose, + field, + root_no_duplicates) attribute = '{http://definition.nexusformat.org/nxdl/3.1}attribute' - root_no_duplicates = yaml2nxdl_backward_tools.compare_niac_and_my(tree, tree2, verbose, - attribute, - root_no_duplicates) + root_no_duplicates = nyaml2nxdl_backward_tools.compare_niac_and_my(tree, tree2, verbose, + attribute, + root_no_duplicates) pretty_print_xml(root_no_duplicates, f"{input_file.replace('.nxdl.xml', '')}" f"_appended.nxdl.xml") print_yml(input_file.replace('.nxdl.xml', '') + "_appended.nxdl.xml", verbose) - yaml2nxdl(input_file.replace('.nxdl.xml', '') + "_appended_parsed.yml", verbose) + nyaml2nxdl(input_file.replace('.nxdl.xml', '') + "_appended_parsed.yml", verbose) os.rename(f"{input_file.replace('.nxdl.xml', '')}_appended_parsed.yml", f"{input_file.replace('.nxdl.xml', '')}_appended.yml") os.rename(f"{input_file.replace('.nxdl.xml', '')}_appended_parsed.nxdl.xml", @@ -446,7 +446,7 @@ def launch_tool(input_file, verbose, append): """ if input_file.rsplit(".", 1)[1] in ('yml', 'yaml'): - yaml2nxdl(input_file, verbose) + nyaml2nxdl(input_file, verbose) if append: append_yml(input_file.rsplit(".", 1)[0] + '.nxdl.xml', append, diff --git a/nexusparser/tools/yaml2nxdl/yaml2nxdl_backward_tools.py b/nexusutils/nyaml2nxdl/nyaml2nxdl_backward_tools.py similarity index 100% rename from nexusparser/tools/yaml2nxdl/yaml2nxdl_backward_tools.py rename to nexusutils/nyaml2nxdl/nyaml2nxdl_backward_tools.py diff --git a/nexusparser/tools/yaml2nxdl/yaml2nxdl_forward_tools.py b/nexusutils/nyaml2nxdl/nyaml2nxdl_forward_tools.py similarity index 99% rename from nexusparser/tools/yaml2nxdl/yaml2nxdl_forward_tools.py rename to nexusutils/nyaml2nxdl/nyaml2nxdl_forward_tools.py index c98567443..3046917c2 100644 --- a/nexusparser/tools/yaml2nxdl/yaml2nxdl_forward_tools.py +++ b/nexusutils/nyaml2nxdl/nyaml2nxdl_forward_tools.py @@ -33,7 +33,7 @@ from yaml.resolver import BaseResolver from yaml.loader import Loader -from nexusparser.tools import nexus +from nexusutils.nexus import nexus NX_CLSS = nexus.get_nx_classes() @@ -113,7 +113,7 @@ def nx_name_type_resolving(tmp): def format_nxdl_doc(string): - """Nexus format for doc string + """NeXus format for doc string """ formatted_doc = '' formatted_doc += f"\n" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..fc8fe17d0 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,57 @@ +[build-system] +requires = ["setuptools>=61.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "nexusutils" +version = "0.0.1" +authors = [ + { name = "The NOMAD Authors" }, +] +description = "Extend NeXus for materials science experiment and serve as a NOMAD parser implementation for NeXus." +readme = "README.md" +license = { file = "LICENSE.txt" } +requires-python = ">=3.7" +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: Apache Software License", + "Operating System :: OS Independent", +] +dependencies = [ + "click>=7.1.2", + "typed-ast>=1.4.2", + "astroid>=2.5.1", + "h5py>=3.6.0", + "xarray>=0.20.2", + "PyYAML>=6.0", + "numpy>=1.21.2", + "pandas>=1.3.2", + "ase>=3.19.0", + "flatdict>=4.0.1", + "hyperspy>=1.7.1", + "jupyterlab_h5web>=6.0.1" +] + +[project.urls] +"Homepage" = "https://github.com/nomad-coe/nomad-parser-nexus" +"Bug Tracker" = "https://github.com/nomad-coe/nomad-parser-nexus/issues" + +[project.optional-dependencies] +dev = [ + "mypy", + "pylint", + "pycodestyle", + "pytest", + "pytest-timeout", + "pytest-cov", + "structlog", + "types-pyyaml" +] + +[project.scripts] +read_nexus = "nexusutils.nexus.nexus:main" +dataconverter = "nexusutils.dataconverter.convert:convert_cli" +nyaml2nxdl = "nexusutils.nyaml2nxdl.nyaml2nxdl:launch_tool" + +[tool.setuptools.package-data] +nexusutils = ["definitions/**/*.xml", "definitions/**/*.xsd"] diff --git a/requirements.txt b/requirements.txt index 50f9c4f58..f87db7a85 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,6 @@ click==7.1.2 -mypy==0.971 +lxml==4.7.1 +mypy==0.750 pylint==2.3.1 pylint_plugin_utils==0.5 typed-ast==1.4.2 @@ -14,7 +15,7 @@ pymongo==3.12.1 h5py==3.6.0 python-json-logger==2.0.2 -xarray==2022.6.0 +xarray==0.20.2 PyYAML==6.0 numpy==1.21.2 pandas==1.3.2 @@ -22,8 +23,4 @@ odfpy==1.4.1 ase==3.19.0 structlog==21.5.0 flatdict==4.0.1 -hyperspy==1.7.1 - -# [nomad] -nomad-lab>=1.1.3 - +hyperspy==1.7.1 \ No newline at end of file diff --git a/setup.py b/setup.py index 66bf48b3c..5fe567178 100644 --- a/setup.py +++ b/setup.py @@ -16,90 +16,6 @@ # limitations under the License. # -from setuptools import setup, find_packages -import os -import re +from setuptools import setup - -def parse_requirements(): - ''' - Parses the requirements.txt file to extras install and extra requirements. - Sections headed with # [extra] are assigned to the 'extra' extra. - - Returns: - Tuple with install and extra requires passible to :func:`setuptools.setup`. - ''' - with open('requirements.txt', 'rt') as f: - lines = f.readlines() - - extras_require = {} - requires = [] - all_requires = [] - current = None - for line in lines: - line = line.strip() - - if line == '': - continue - - match = re.match(r'^#\s*\[([a-zA-Z0-9_]+)\]$', line) - if match: - extra = match.group(1) - current = list() - extras_require[extra] = current - elif line.startswith('#'): - continue - else: - line = line.split('#')[0].strip() - if current is None: - requires.append(line) - else: - current.append(line) - all_requires.append(line) - - extras_require['all'] = all_requires - - return requires, extras_require - -def main(): - try: - for nexus_definition_dir in ("/./", "/base_classes/", "/applications/", "/contributed_definitions/"): - f = open(os.path.abspath(os.path.dirname(__file__)) + "/nexusparser/definitions/" + nexus_definition_dir + "__init__.py", "a") - f.close() - except FileNotFoundError: - pass - - with open("README.md", "r") as f: - long_description = f.read() - - requires, extras_require = parse_requirements() - - setup( - name='nexusparser', - version='0.0.1', - description='NOMAD parser implementation for Nexus.', - long_description=long_description, - long_description_content_type="text/markdown", - author='The NOMAD Authors', - license='APACHE 2.0', - packages=find_packages(exclude=['tests']), - package_data={ - 'nexusparser.definitions.base_classes': ['*.xml'], - 'nexusparser.definitions.applications': ['*.xml'], - 'nexusparser.definitions.contributed_definitions': ['*.xml'], - 'nexusparser.definitions': ['*.xsd'] - }, - include_package_data=True, - install_requires=requires, - extras_require=extras_require, - entry_points={ - 'console_scripts': [ - 'read_nexus = nexusparser.tools.nexus:main', - 'dataconverter = nexusparser.tools.dataconverter.convert:convert_cli', - 'yaml2nxdl = nexusparser.tools.yaml2nxdl.yaml2nxdl:launch_tool' - ] - }) - - -if __name__ == '__main__': - main() +setup() \ No newline at end of file diff --git a/tests/data/tools/dataconverter/NXtest.nxdl.xml b/tests/data/dataconverter/NXtest.nxdl.xml similarity index 100% rename from tests/data/tools/dataconverter/NXtest.nxdl.xml rename to tests/data/dataconverter/NXtest.nxdl.xml diff --git a/tests/data/dataconverter/readers/apm/README.md b/tests/data/dataconverter/readers/apm/README.md new file mode 100644 index 000000000..3d6bc0db8 --- /dev/null +++ b/tests/data/dataconverter/readers/apm/README.md @@ -0,0 +1,2 @@ +This is a place for storing data for tests which verify the functionality of the apm reader. +An example for how to use the apm reader is available in *nomad-parser-nexus/examples/apm*. \ No newline at end of file diff --git a/tests/data/tools/dataconverter/readers/apm/nomad_oasis_eln_schema_for_nx_apm/nxapm.schema.archive.yaml b/tests/data/dataconverter/readers/apm/nomad_oasis_eln_schema_for_nx_apm/nxapm.schema.archive.yaml similarity index 100% rename from tests/data/tools/dataconverter/readers/apm/nomad_oasis_eln_schema_for_nx_apm/nxapm.schema.archive.yaml rename to tests/data/dataconverter/readers/apm/nomad_oasis_eln_schema_for_nx_apm/nxapm.schema.archive.yaml diff --git a/tests/data/tools/dataconverter/readers/ellips/README.md b/tests/data/dataconverter/readers/ellips/README.md similarity index 100% rename from tests/data/tools/dataconverter/readers/ellips/README.md rename to tests/data/dataconverter/readers/ellips/README.md diff --git a/tests/data/dataconverter/readers/ellips/eln_data.yaml b/tests/data/dataconverter/readers/ellips/eln_data.yaml new file mode 100644 index 000000000..6b0c7e733 --- /dev/null +++ b/tests/data/dataconverter/readers/ellips/eln_data.yaml @@ -0,0 +1,71 @@ +acquisition_program/\@url: https://www.jawoollam.com/ellipsometry-software/wvase +acquisition_program/program: WVASE +acquisition_program/version: '3.882' +address: Zum Großen Windkanal 2, 12489 Berlin, Germany +affiliation: Humboldt-Universität zu Berlin +angle_of_incidence_unit: degrees +angular_spread: + unit: rad ** 2 + value: 0.2 +atom_types: Si, O +blocks: +- type +- angle_of_incidence +calibration_status: no calibration +colnames: +- type +- wavelength +- angle_of_incidence +- psi +- delta +- err.psi +- err.delta +column_names: +- psi +- delta +company: J. A. Woollam Co. +count_time: + unit: s + value: 1 +data_identifier: 1 +data_type: psi/delta +definition: NXellipsometry +definition/\@url: https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat-ellips/contributed_definitions/NXellipsometry.nxdl.xml +definition/\@version: 0.0.2 +detector_type: CCD spectrometer +ellipsometry_type: dual compensator +email: surname.name@physik.hu-berlin.de +err-var: +- err.psi +- err.delta +experiment_description: RC2 scan on 2nm SiO2 on Si in air +experiment_identifier: exp-ID +filename: test-data.dat +firmware: CompleteEASE +firmware/\@url: https://www.jawoollam.com/ellipsometry-software/completeease +firmware/\@version: '6.37' +focussing_probes: false +integration_time: + unit: s + value: 0 +layer_structure: 2nm SiO2 on Si +light_source: arc lamp +medium: air +model: RC2 +model/\@version: 0.0.1 +name: Name Surname +parameters: +- type +- angle +rotating_element: compensator (source side) +sample_history: Commercially purchased sample +sample_name: 2nm SiO2 on Si +sep: \t +skip: 3 +stage_type: manual stage +start_time: '2022-01-27T04:35:00+00:00' +wavelength_unit: angstrom +x-var: wavelength +y-var: +- psi +- delta diff --git a/tests/data/dataconverter/readers/ellips/test-data.dat b/tests/data/dataconverter/readers/ellips/test-data.dat new file mode 100644 index 000000000..211871453 --- /dev/null +++ b/tests/data/dataconverter/readers/ellips/test-data.dat @@ -0,0 +1,9795 @@ +2nm SiO2 on Si on RC2 +VASEmethod[EllipsometerType=4 , CompleteEASE=6.37, AcqTime=15.000, ZoneAve=1, Acq. Parameters=DEFAULT.parms,WinCorrected=1] +Angstroms +E 1930.000000 50.000000 40.014217 142.127655 0.008585 0.034774 +E 1940.000000 50.000000 40.026409 142.307449 0.007827 0.031627 +E 1950.000000 50.000000 40.031204 142.483231 0.007221 0.029106 +E 1960.000000 50.000000 40.045902 142.679901 0.006813 0.027399 +E 1970.000000 50.000000 40.065468 142.866608 0.006478 0.025995 +E 1980.000000 50.000000 40.077728 143.102463 0.006224 0.024925 +E 1990.000000 50.000000 40.080673 143.409317 0.006016 0.024045 +E 2000.000000 50.000000 40.082367 143.746017 0.005829 0.023258 +E 2010.000000 50.000000 40.072388 143.990952 0.005649 0.022496 +E 2020.000000 50.000000 40.073170 144.279099 0.005475 0.021767 +E 2030.000000 50.000000 40.069405 144.611435 0.005311 0.021084 +E 2040.000000 50.000000 40.066757 144.883820 0.005150 0.020417 +E 2050.000000 50.000000 40.061028 145.150055 0.004993 0.019760 +E 2060.000000 50.000000 40.055706 145.396118 0.004843 0.019128 +E 2070.000000 50.000000 40.036533 145.661514 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70.000000 -0.217532 0.147289 +dPolE 16925.000000 70.000000 -0.622895 0.173056 +dPolE 16950.000000 70.000000 -0.393209 0.199934 +dPolE 16975.000000 70.000000 -0.096587 0.228777 +dPolE 17000.000000 70.000000 0.152324 0.260383 \ No newline at end of file diff --git a/tests/data/tools/dataconverter/readers/em_nion/EmNion.NeXus.NXem.Example.1.ipynb b/tests/data/dataconverter/readers/em_nion/EmNion.NeXus.NXem.Example.1.ipynb similarity index 100% rename from tests/data/tools/dataconverter/readers/em_nion/EmNion.NeXus.NXem.Example.1.ipynb rename to tests/data/dataconverter/readers/em_nion/EmNion.NeXus.NXem.Example.1.ipynb diff --git a/tests/data/tools/dataconverter/readers/em_nion/HAADF_01.ELabFTW.dat b/tests/data/dataconverter/readers/em_nion/HAADF_01.ELabFTW.dat similarity index 100% rename from tests/data/tools/dataconverter/readers/em_nion/HAADF_01.ELabFTW.dat rename to tests/data/dataconverter/readers/em_nion/HAADF_01.ELabFTW.dat diff --git a/tests/data/tools/dataconverter/readers/em_nion/HAADF_01.json b/tests/data/dataconverter/readers/em_nion/HAADF_01.json similarity index 100% rename from tests/data/tools/dataconverter/readers/em_nion/HAADF_01.json rename to tests/data/dataconverter/readers/em_nion/HAADF_01.json diff --git a/tests/data/tools/dataconverter/readers/em_nion/HAADF_01.npy b/tests/data/dataconverter/readers/em_nion/HAADF_01.npy similarity index 100% rename from tests/data/tools/dataconverter/readers/em_nion/HAADF_01.npy rename to tests/data/dataconverter/readers/em_nion/HAADF_01.npy diff --git a/tests/data/tools/dataconverter/readers/em_nion/eln_data.yaml b/tests/data/dataconverter/readers/em_nion/eln_data.yaml similarity index 100% rename from tests/data/tools/dataconverter/readers/em_nion/eln_data.yaml rename to tests/data/dataconverter/readers/em_nion/eln_data.yaml diff --git a/tests/data/dataconverter/readers/em_spctrscpy/README.md b/tests/data/dataconverter/readers/em_spctrscpy/README.md new file mode 100644 index 000000000..3f79a7b51 --- /dev/null +++ b/tests/data/dataconverter/readers/em_spctrscpy/README.md @@ -0,0 +1,2 @@ +This is a place for storing data for tests which verify the functionality of the em_spctrscpy reader. +An example for how to use the em_spctrscpy reader is available in *nomad-parser-nexus/examples/em*. \ No newline at end of file diff --git a/tests/data/tools/dataconverter/readers/em_spctrscpy/nomad_oasis_eln_schema_for_nx_em/eln_data_em.yaml b/tests/data/dataconverter/readers/em_spctrscpy/nomad_oasis_eln_schema_for_nx_em/eln_data_em.yaml similarity index 100% rename from tests/data/tools/dataconverter/readers/em_spctrscpy/nomad_oasis_eln_schema_for_nx_em/eln_data_em.yaml rename to tests/data/dataconverter/readers/em_spctrscpy/nomad_oasis_eln_schema_for_nx_em/eln_data_em.yaml diff --git a/tests/data/tools/dataconverter/readers/em_spctrscpy/nomad_oasis_eln_schema_for_nx_em/nxem.schema.archive.yaml b/tests/data/dataconverter/readers/em_spctrscpy/nomad_oasis_eln_schema_for_nx_em/nxem.schema.archive.yaml similarity index 100% rename from tests/data/tools/dataconverter/readers/em_spctrscpy/nomad_oasis_eln_schema_for_nx_em/nxem.schema.archive.yaml rename to tests/data/dataconverter/readers/em_spctrscpy/nomad_oasis_eln_schema_for_nx_em/nxem.schema.archive.yaml diff --git a/tests/data/tools/dataconverter/readers/example/testdata.json b/tests/data/dataconverter/readers/example/testdata.json similarity index 100% rename from tests/data/tools/dataconverter/readers/example/testdata.json rename to tests/data/dataconverter/readers/example/testdata.json diff --git a/tests/data/tools/dataconverter/readers/json_map/data.json b/tests/data/dataconverter/readers/json_map/data.json similarity index 100% rename from tests/data/tools/dataconverter/readers/json_map/data.json rename to tests/data/dataconverter/readers/json_map/data.json diff --git a/tests/data/tools/dataconverter/readers/json_map/data.mapping.json b/tests/data/dataconverter/readers/json_map/data.mapping.json similarity index 100% rename from tests/data/tools/dataconverter/readers/json_map/data.mapping.json rename to tests/data/dataconverter/readers/json_map/data.mapping.json diff --git a/tests/data/tools/dataconverter/readers/mpes/ELN_metadata_example.yaml b/tests/data/dataconverter/readers/mpes/ELN_metadata_example.yaml similarity index 100% rename from tests/data/tools/dataconverter/readers/mpes/ELN_metadata_example.yaml rename to tests/data/dataconverter/readers/mpes/ELN_metadata_example.yaml diff --git a/tests/data/tools/dataconverter/readers/mpes/Ref_nexus_mpes.log b/tests/data/dataconverter/readers/mpes/Ref_nexus_mpes.log similarity index 100% rename from tests/data/tools/dataconverter/readers/mpes/Ref_nexus_mpes.log rename to tests/data/dataconverter/readers/mpes/Ref_nexus_mpes.log diff --git a/tests/data/tools/dataconverter/readers/mpes/config_file.json b/tests/data/dataconverter/readers/mpes/config_file.json similarity index 100% rename from tests/data/tools/dataconverter/readers/mpes/config_file.json rename to tests/data/dataconverter/readers/mpes/config_file.json diff --git a/tests/data/tools/dataconverter/readers/mpes/xarray_saved_small_calibration.h5 b/tests/data/dataconverter/readers/mpes/xarray_saved_small_calibration.h5 similarity index 100% rename from tests/data/tools/dataconverter/readers/mpes/xarray_saved_small_calibration.h5 rename to tests/data/dataconverter/readers/mpes/xarray_saved_small_calibration.h5 diff --git a/tests/data/tools/dataconverter/readers/transmission/KTF-9_1_A.asc b/tests/data/dataconverter/readers/transmission/KTF-9_1_A.asc similarity index 100% rename from tests/data/tools/dataconverter/readers/transmission/KTF-9_1_A.asc rename to tests/data/dataconverter/readers/transmission/KTF-9_1_A.asc diff --git a/tests/data/tools/dataconverter/readers/transmission/KTF-9_1_A.sp b/tests/data/dataconverter/readers/transmission/KTF-9_1_A.sp similarity index 100% rename from tests/data/tools/dataconverter/readers/transmission/KTF-9_1_A.sp rename to tests/data/dataconverter/readers/transmission/KTF-9_1_A.sp diff --git a/tests/data/tools/dataconverter/readers/transmission/metadata.json b/tests/data/dataconverter/readers/transmission/metadata.json similarity index 100% rename from tests/data/tools/dataconverter/readers/transmission/metadata.json rename to tests/data/dataconverter/readers/transmission/metadata.json diff --git a/tests/data/nexus_test_data/201805_WSe2_arpes.nxs b/tests/data/nexus/201805_WSe2_arpes.nxs similarity index 100% rename from tests/data/nexus_test_data/201805_WSe2_arpes.nxs rename to tests/data/nexus/201805_WSe2_arpes.nxs diff --git a/tests/data/nexus_test_data/Ref_nexus_test.log b/tests/data/nexus/Ref_nexus_test.log similarity index 99% rename from tests/data/nexus_test_data/Ref_nexus_test.log rename to tests/data/nexus/Ref_nexus_test.log index 7576510ef..d8d2ac50e 100644 --- a/tests/data/nexus_test_data/Ref_nexus_test.log +++ b/tests/data/nexus/Ref_nexus_test.log @@ -1,4 +1,3 @@ -DEBUG - Creating converter from 3 to 5 DEBUG - ===== GROUP (//entry [NXarpes::/NXentry]): DEBUG - classpath: ['NXentry'] DEBUG - classes: diff --git a/tests/data/nexus.out b/tests/data/nexus/nexus.out similarity index 100% rename from tests/data/nexus.out rename to tests/data/nexus/nexus.out diff --git a/tests/data/tools/yaml2nxdl_test_data/NXattributes.yml b/tests/data/nyaml2nxdl/NXattributes.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/NXattributes.yml rename to tests/data/nyaml2nxdl/NXattributes.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/NXellipsometry-docCheck.yaml b/tests/data/nyaml2nxdl/NXellipsometry-docCheck.yaml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/NXellipsometry-docCheck.yaml rename to tests/data/nyaml2nxdl/NXellipsometry-docCheck.yaml diff --git a/tests/data/tools/yaml2nxdl_test_data/NXfilelineError1.yml b/tests/data/nyaml2nxdl/NXfilelineError1.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/NXfilelineError1.yml rename to tests/data/nyaml2nxdl/NXfilelineError1.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/NXfilelineError2.yml b/tests/data/nyaml2nxdl/NXfilelineError2.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/NXfilelineError2.yml rename to tests/data/nyaml2nxdl/NXfilelineError2.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/NXfilelineError3.yml b/tests/data/nyaml2nxdl/NXfilelineError3.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/NXfilelineError3.yml rename to tests/data/nyaml2nxdl/NXfilelineError3.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/NXmytests.yml b/tests/data/nyaml2nxdl/NXmytests.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/NXmytests.yml rename to tests/data/nyaml2nxdl/NXmytests.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/NXnested_symbols.yml b/tests/data/nyaml2nxdl/NXnested_symbols.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/NXnested_symbols.yml rename to tests/data/nyaml2nxdl/NXnested_symbols.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/NXtest_links.yml b/tests/data/nyaml2nxdl/NXtest_links.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/NXtest_links.yml rename to tests/data/nyaml2nxdl/NXtest_links.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXattributes.nxdl.xml b/tests/data/nyaml2nxdl/Ref_NXattributes.nxdl.xml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXattributes.nxdl.xml rename to tests/data/nyaml2nxdl/Ref_NXattributes.nxdl.xml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXellips.nxdl.xml b/tests/data/nyaml2nxdl/Ref_NXellips.nxdl.xml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXellips.nxdl.xml rename to tests/data/nyaml2nxdl/Ref_NXellips.nxdl.xml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry-docCheck.nxdl.xml b/tests/data/nyaml2nxdl/Ref_NXellipsometry-docCheck.nxdl.xml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry-docCheck.nxdl.xml rename to tests/data/nyaml2nxdl/Ref_NXellipsometry-docCheck.nxdl.xml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry.yml b/tests/data/nyaml2nxdl/Ref_NXellipsometry.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry.yml rename to tests/data/nyaml2nxdl/Ref_NXellipsometry.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXentry.nxdl.xml b/tests/data/nyaml2nxdl/Ref_NXentry.nxdl.xml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXentry.nxdl.xml rename to tests/data/nyaml2nxdl/Ref_NXentry.nxdl.xml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXentry.yml b/tests/data/nyaml2nxdl/Ref_NXentry.yml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXentry.yml rename to tests/data/nyaml2nxdl/Ref_NXentry.yml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXmytests.nxdl.xml b/tests/data/nyaml2nxdl/Ref_NXmytests.nxdl.xml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXmytests.nxdl.xml rename to tests/data/nyaml2nxdl/Ref_NXmytests.nxdl.xml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXnested_symbols.nxdl.xml b/tests/data/nyaml2nxdl/Ref_NXnested_symbols.nxdl.xml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXnested_symbols.nxdl.xml rename to tests/data/nyaml2nxdl/Ref_NXnested_symbols.nxdl.xml diff --git a/tests/data/tools/yaml2nxdl_test_data/Ref_NXtest_links.nxdl.xml b/tests/data/nyaml2nxdl/Ref_NXtest_links.nxdl.xml similarity index 100% rename from tests/data/tools/yaml2nxdl_test_data/Ref_NXtest_links.nxdl.xml rename to tests/data/nyaml2nxdl/Ref_NXtest_links.nxdl.xml diff --git a/tests/data/tools/dataconverter/readers/apm/Apm.NeXus.Apm.Example.1.ipynb b/tests/data/tools/dataconverter/readers/apm/Apm.NeXus.Apm.Example.1.ipynb deleted file mode 100644 index 2f2e6eb3f..000000000 --- a/tests/data/tools/dataconverter/readers/apm/Apm.NeXus.Apm.Example.1.ipynb +++ /dev/null @@ -1,419 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## NOMAD-PARSER-NEXUS/DATACONVERTER demo for Atom Probe Microscopy (APM) data" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step 1:** Check that everything is ready to go and download example data for APM. " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! pip list | grep 'nomad\\|nexus' && jupyter serverextension list && jupyter labextension list && python -V" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Set the nexusparser directory." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import os\n", - "import nexusparser\n", - "nexus_dir = os.path.dirname(nexusparser.__file__)\n", - "print(nexus_dir)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### **Step 2:** Download APM-specific example data." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "For this case, the data can be found in zenodo." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import shutil # unpacks in current path unless an additional path argument is provided" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# http://dx.doi.org/10.5281/zenodo.6808516\n", - "! curl --output APM.LEAP.Datasets.1.zip https://zenodo.org/record/6808516/files/APM.LEAP.Datasets.1.zip\n", - "shutil.unpack_archive('APM.LEAP.Datasets.1.zip')" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "These files should serve exclusively as examples. The dataconverter for APM always requires a triplet of files:\n", - "* A **community or vendor file** with the ion positions and mass-to-charge state ratio values for the tomographic reconstruction. POS, ePOS, or APT are allowed.\n", - "* A file with **ranging definitions**, i.e. how mass-to-charge-state ratio values map on ion species. RNG or RRNG are allowed.\n", - "* A **file with additional metadata (edited manually or via an ELN) in YAML format**. The eln_data_apm.yaml file in the example can be edited with a text editor.\n", - "For GUI-based editing, a NOMAD OASIS instance is needed.
\n", - "Please note that the metadata inside the provided eln_data_apm.yaml file has example data in it.\n", - "These reflect not necessarily the conditions when the raw data for the example were given. The file is meant to be edited!" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step 3:** Run your APM-specific dataconverter/readers/ on the example data." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now we run our parser. The --reader flag takes the atom probe microscopy reader (apm), the --nxdl flag takes the application definition for this technique.
" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Inspect what can/should be in the NeXus file." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! echo {nexus_dir}" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### **Step 3a:** Optionally see the command line help of the dataconverter." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! python3 {nexus_dir}/tools/dataconverter/convert.py --help" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### **Step 3b:** Optionally explore all paths which NXapm provides." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "# to inspect what can/should all be in the NeXus file\n", - "! python3 {nexus_dir}/tools/dataconverter/convert.py --nxdl NXapm --generate-template" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### **Step 3c**: Convert the files in the example into an NXapm-compliant NeXus HDF5 file." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "! python3 {nexus_dir}/tools/dataconverter/convert.py \\\n", - "--reader apm \\\n", - "--nxdl NXapm \\\n", - "--input-file R31_06365-v02.pos \\\n", - "--input-file R31_06365-v02.rrng \\\n", - "--input-file eln_data_apm.yaml \\\n", - "--output usa_pos.nxs" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The key take home message is that the command above-specified triggers the automatic creation of the HDF5 file. This *.nxs file, is an HDF5 file." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step 4:** Inspect the HDF5/NeXus file apm*.test.nxs using H5Web." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from jupyterlab_h5web import H5Web" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "h5_file_name = 'usa_pos.nxs'" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "H5Web(h5_file_name)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "You can also visualize the .nxs file by double clicking on it in the file explorer panel to the left side of your jupyter lab screen in the browser." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step 5:** Optionally, do some post-processing with the generated usa_pos.nxs file." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "To compute a mass-to-charge histogram and explore eventual ranging definitions that have also been carried over in the conversion step (step 6)." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import numpy as np\n", - "import matplotlib.pyplot as plt\n", - "from matplotlib.collections import PatchCollection\n", - "from matplotlib.patches import Rectangle\n", - "plt.rcParams['figure.figsize'] = [20, 10]\n", - "plt.rcParams['figure.dpi'] = 300\n", - "import h5py as h5\n", - "#needs shutils for decompressing zip archives, which is a default module/package in Python since >=v3.6" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Read mass-to-charge-state ratio values, create a histogram (\"mass spectrum\"), and mark ranges." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# load data and ranges\n", - "hf = h5.File(h5_file_name, 'r')\n", - "mq = hf['entry/atom_probe/mass_to_charge_conversion/mass_to_charge'][:]\n", - "nions = np.uint32(hf['entry/atom_probe/ranging/number_of_ion_types'])\n", - "print('Array with mass-to-charge-state ratios loaded')\n", - "print(str(nions) + ' iontypes were distinguished')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# define binning\n", - "[mqmin, mqmax] = [0., 100.0] # Da np.max(mq)]\n", - "print('Dataset ranging from [' + str(mqmin) + ', ' + str(mqmax) +'] Da.')\n", - "mqincr = 0.01 #Da\n", - "print('Using a mass-to-charge-state ratio resolution of '+str(mqincr)+' Da.')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# transform collection of mass-to-charge-state ratios into a histogram\n", - "hst1d = np.unique(np.uint64(np.floor((mq[np.logical_and(mq >= mqmin, mq <= mqmax)] - mqmin) / mqincr)), return_counts=True)\n", - "nbins = np.uint64((mqmax - mqmin) / mqincr + 1)\n", - "print('Histogram has ' + str(nbins) + ' bins.')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "# use matplotlib and numpy to plot histogram data \n", - "xy = np.zeros([nbins, 2], np.float64)\n", - "xy[:,0] = np.linspace(mqmin + mqincr, mqmax + mqincr, nbins, endpoint=True)\n", - "xy[:,1] = 0.5 # * np.ones([nbins], np.float64) # 0.5 to be able to plot logarithm you can not measure half an atom\n", - "for i in np.arange(0, len(hst1d[0])):\n", - " binidx = hst1d[0][i]\n", - " xy[binidx, 1] = hst1d[1][i]\n", - "print('Mass-to-charge-state histogram created.')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "[xmi, xmx, ymi, ymx] = [mqmin, 10**np.ceil(np.log10(mqmax)), 0.5, 10**np.ceil(np.log10(np.max(xy[:,1])))]\n", - "[xmi, xmx, ymi, ymx] = [mqmin, mqmax, 0.5, 10**np.ceil(np.log10(np.max(xy[:,1])))]\n", - "fig, cnts_over_mq = plt.subplots(1, 1)\n", - "plt.plot(xy[:, 0], xy[:, 1], color='blue', alpha=0.5, linewidth=1.0)\n", - "for i in np.arange(1,nions + 1):\n", - " # load ranges and plot them\n", - " ranges = hf['entry/atom_probe/ranging/peak_identification/ion' + str(i) + '/mass_to_charge_range'][:]\n", - " for min_max in ranges:\n", - " cnts_over_mq.vlines(min_max[0], 0, 1, transform=cnts_over_mq.get_xaxis_transform(), alpha=0.1, color='grey', linestyles='dotted')\n", - " cnts_over_mq.vlines(min_max[1], 0, 1, transform=cnts_over_mq.get_xaxis_transform(), alpha=0.1, color='grey', linestyles='dotted')\n", - " #rng = Rectangle((min_max[0], ymi), min_max[1] - min_max[0], ymx - ymi, edgecolor='r', facecolor=\"none\")\n", - "# plt.xticks([1, 2, 3, 4, 5, 6, 7, 8, 9], ['Min', '0.0025', '0.025', '0.25', '0.50', '0.75', '0.975', '0.9975', 'Max'])\n", - "plt.yscale('log')\n", - "plt.legend( [r'Mass-to-charge-state ratio $\\Delta\\frac{m}{q} = $'+str(mqincr)+' Da'], loc='upper right')\n", - "plt.xlabel(r'Mass-to-charge-state-ratio (Da)')\n", - "plt.ylabel(r'Counts')\n", - "print('Mass-to-charge-state histogram visualized.')\n", - "# scale bar with add margin to the bottom and top of the yaxis to avoid that lines fall on x axis\n", - "margin=0.01 # polishing the margins\n", - "plt.xlim([-margin * (xmx - xmi) + xmi, +margin * (xmx - xmi) + xmx])\n", - "plt.ylim([ymi, +margin * (ymx - ymi) + ymx])" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "#save the figure\n", - "figfn = h5_file_name + '.MassToChargeStateRatios.png'\n", - "fig.savefig(figfn, dpi=300, facecolor='w', edgecolor='w', orientation='landscape', format='png', \n", - " transparent=False, bbox_inches='tight', pad_inches=0.1, metadata=None)\n", - "#plt.close('all')\n", - "print(figfn + ' stored to disk.')" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### Further comments:" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "* Feel free to explore our atom probe microscopy containers in the north branch for more advanced processing" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "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": "3.8.10" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/tests/data/tools/dataconverter/readers/ellips/ELLIPSOMETRY.NeXus.READER.EXAMPLE.02.ipynb b/tests/data/tools/dataconverter/readers/ellips/ELLIPSOMETRY.NeXus.READER.EXAMPLE.02.ipynb deleted file mode 100644 index 820d6c12f..000000000 --- a/tests/data/tools/dataconverter/readers/ellips/ELLIPSOMETRY.NeXus.READER.EXAMPLE.02.ipynb +++ /dev/null @@ -1,307 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## nomad-parser-nexus demo for Ellipsometry data" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "jp-MarkdownHeadingCollapsed": true, - "tags": [] - }, - "source": [ - "### **Step -1:** Create a new virtual environment and set up dependencies for jupyterlab_h5web.
This section **should only be run if you do not have Jupyter Lab, its extensions and the extra needed packages.**
For use within the Nomad UI this section should be skipped.
These cells can be run in a Jupyter notebook or copied to a terminal without the \"!\"." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Run the following to start with a fresh virtualenv in **your terminal** in which you are installing and then running **Jupyter lab** if you wish to:
\n", - "```pip install virtualenv && virtualenv --python=python3.7 .nexusenv && source .nexusenv/bin/activate```" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Install jupyter, jupyter-lab and h5web extensions." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! pip install --upgrade nodejs && pip install ipywidgets h5py==3.5.0 h5glance==0.7 h5grove==0.0.14 jupyterlab[full]==3.2.9 jupyterlab_h5web[full]==1.3.0 punx==0.2.5 nexpy==0.14.1 silx[full]==1.0.0 && jupyter lab build" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Enable the extensions" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! jupyter nbextension enable --py widgetsnbextension" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "! jupyter serverextension enable jupyterlab_h5web" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "jp-MarkdownHeadingCollapsed": true, - "tags": [] - }, - "source": [ - "### **Step 0:** Installing and testing nomad-parser-nexus module.
This section **should only be run if you are not running this within NOMAD.**
" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Install nomad and its dependencies. Do not run the following cell if you have a nomad installation running. " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "! pip install --upgrade pip && pip install nomad-lab==1.0.0 --extra-index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple\n", - "! pip list" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Install the nexusparser and its requirements" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! git clone https://github.com/nomad-coe/nomad-parser-nexus.git --recursive && cd nomad-parser-nexus && git status && pip install -r requirements.txt && pip install -e .[all]" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The following cell restarts the kernel after the nexusparser installation" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import os\n", - "os._exit(00)" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "jp-MarkdownHeadingCollapsed": true, - "tags": [] - }, - "source": [ - "### **Step 1:** Check that everything is ready to go and look for example data for Ellipsometry. " - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "Check dependencies of nomad and of the nexusparser and prints them. If the nexusparser and nomad-lab are installed, you are ready to go.
Check if jupyterlab_h5web server and lab extensions are enabled and OK. " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! pip list | grep 'nomad\\|nexus'\n", - "! jupyter serverextension list\n", - "! jupyter labextension list" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "For this case, the data can be found in the current working directory." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "jp-MarkdownHeadingCollapsed": true, - "tags": [] - }, - "source": [ - "### **Step 2:** Run your ellipsometry-specific dataconverter/readers/ on the example data" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Set the nexusparser directory." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import os\n", - "import nexusparser\n", - "nexus_dir = os.path.dirname(nexusparser.__file__) # where the nexusparser module is located!!!!\n", - "print(nexus_dir)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now we run our parser. The --reader flag takes the ellipsometry reader (ellips), the --nxdl flag takes the application definition for this technique.
" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "! python3 {nexus_dir}/tools/dataconverter/convert.py \\\n", - "--reader ellips \\\n", - "--nxdl NXellipsometry \\\n", - "--input-file test.yaml \\\n", - "--output ellips.test.nxs" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The command in the cell above has created an HDF5 file. This *.nxs file, is an HDF5 file." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "jp-MarkdownHeadingCollapsed": true, - "tags": [] - }, - "source": [ - "### **Step 3:** Inspect the HDF5/NeXus file apm.test.nxs using H5Web" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from jupyterlab_h5web import H5Web" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "H5Web('ellips.test.nxs')" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Here is where the general template ends. Continue to fill the notebook based on
\n", - "**your own** post-processing of the *.nxs file." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "jp-MarkdownHeadingCollapsed": true, - "tags": [] - }, - "source": [ - "### **Step 4:** Extract for instance data inside ellips.test.nxs and to post processing (to be done for this particular case)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "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": "3.7.12" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/tests/data/tools/dataconverter/readers/ellips/test.yaml b/tests/data/tools/dataconverter/readers/ellips/test.yaml deleted file mode 100644 index 16e77952e..000000000 --- a/tests/data/tools/dataconverter/readers/ellips/test.yaml +++ /dev/null @@ -1,91 +0,0 @@ -#filename: tests/data/tools/dataconverter/readers/ellips/test-data.dat -filename: test-data.dat -skip: 3 -sep: "\t" - -# if the file has a block structure, -# which column has the block index? -blocks: - - type - - angle_of_incidence - -colnames: - - type - - wavelength - - angle_of_incidence - - psi - - delta - - err.psi - - err.delta -x-var: wavelength -y-var: - - psi - - delta -err-var: - - err.psi - - err.delta -parameters: - - type - - angle - -definition: NXellipsometry -definition/\@version: 0.0.2 -definition/\@url: https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat-ellips/contributed_definitions - -experiment_identifier: exp-ID -experiment_description: RC2 scan on 2nm SiO2 on Si in air -start_time: "2022-01-27T12:05:35+00:00" - -acquisition_program/program: CompleteEASE -acquisition_program/version: "6.37" -acquisition_program/\@url: https://www.jawoollam.com/ellipsometry-software/completeease - -name: Name Surname -affiliation: HU Berlin -address: Unter den Linden -email: name@hu-berlin.de - -# NXinstrument: -model: RC2 -model/\@version: 0.0.1 -company: J.A. Woollam Co. -firmware: WVASE -firmware/\@version: 3.882 -firmware/\@url: https://www.jawoollam.com/ellipsometry-software/wvase -light_source: arc lamp -#light_source/target_material: Xe -focussing_probes: false -angular_spread: 0.2 -angular_spread/@units: sr -ellipsometry_type: dual compensator -calibration_status: no calibration -stage_type: manual stage -detector_type: CCD spectrometer -count_time: 1 -count_time/\@units: s -integration_time: 0 -integration_time/\@units: s -rotating_element: compensator (source side) -# TAKE care: if you use the yaml list syntax, you'll break the -# reader tests, check the reader code -# - compensator (source side) -# - compensator (detector side) -# Should be both compensators, source and detector side. -# needs to be taken care of in the reader - -# Angle of incidence and wavelength are read by the reader -# and we just have to define the units here: -angle_of_incidence/\@units: "degrees" -wavelength/\@units: "angstrom" - -# NXsample: -atom_types: Si, O -sample_name: 2nm SiO2 on Si -sample_history: Commercially purchased sample -layer_structure: 2nm SiO2 on Si -data_identifier: 1 -data_type: psi/delta -column_names: - - psi - - delta -medium: air diff --git a/tests/data/tools/dataconverter/readers/em_spctrscpy/README.md b/tests/data/tools/dataconverter/readers/em_spctrscpy/README.md deleted file mode 100644 index 7a844f698..000000000 --- a/tests/data/tools/dataconverter/readers/em_spctrscpy/README.md +++ /dev/null @@ -1,82 +0,0 @@ -The tools of the NOMAD parser for [NEXUS](https://www.nexusformat.org/) can also be used -without a NOMAD OASIS installation. There are two main use cases: -- Use the DATACONVERTER/em_spctrscpy for transcoding vendor and community files to - NeXus files so that these are compliant with a specific NeXus application definition - [NEXUS-FAIRMAT-PROPOSAL](https://fairmat-experimental.github.io/nexus-fairmat-proposal/). - In this example NXem. -- Use the YAML2NXDL converter during editing and developing - NeXus base classes and application definitions. - -## Getting started - prepare your environment - -It is recommended to install the tool in an own virtual environment as -some installation steps will install specific versions of packages which -might be in conflict with existent ones in your environment. -You can install the tools as standalone tools. We make the following assumptions: -- You have a python in version 3.7 installed. Higher versions can be used but might - need modifications for specific packages on which nomad-parser-nexus depends. -- You can but do not need to be inside a conda environment. - -``` -pip install virtualenv && virtualenv --python=python3.7 .nexusenv && source .nexusenv/bin/activate -pip install --upgrade pip==22.2.2 && pip install --upgrade nodejs==0.1.1 -pip install jupyterlab_h5web[full]==6.0.1 -``` - -## Getting started - install the nomad-parser-nexus tool - -``` -git clone https://github.com/nomad-coe/nomad-parser-nexus.git --recursive -cd nomad-parser-nexus/ -git branch -a -pip install -e . -``` - -With these two steps the installation is complete. - -### Using the tool - -The tool can be used as a command line application or started within jupyter lab: - -``` -jupyter lab -``` - -If you are using a Linux operating system, a browser tab should open up -which shows the running jupyter lab instance. If you are on Windows and use WSL2, - -this command into the command line will leave you with a message in the -console reading: - -``` -... -Jupyter Server <> is running at. -http://localhost:8888/lab?token=<> -... - -``` - -You should copy this localhost address into your browser, so that you can also -see the running jupyter lab instance and interact with it graphically. - -If you are on Windows and use WSL2 an error will follow after the localhost address, -which can be ignored though. - -It can happen that H5Web visualizations show differences across web browsers. -We observed that for some configurations the H5Web plots are displayed -cleaner for the chrome browser than for firefox. - -### Calling the DATACONVERTER - -There is a jupyter notebook (ipynb) for each technique which you should -use to interact with the tool. - -## Where should one place the files -For the dataconverter, you can find the respective notebooks in - -``` -tests/data/tools/dataconverter/readers/em-spctrscpy/ -``` - -Go one directory deeper to explore the specific jupyter notebook for your method of choice. - diff --git a/tests/data/tools/dataconverter/readers/mpes/mpes.NeXus.mpes.Example.1.ipynb b/tests/data/tools/dataconverter/readers/mpes/mpes.NeXus.mpes.Example.1.ipynb deleted file mode 100644 index 8ab1e29c2..000000000 --- a/tests/data/tools/dataconverter/readers/mpes/mpes.NeXus.mpes.Example.1.ipynb +++ /dev/null @@ -1,331 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## nomad-parser-nexus demo for Multidimensional Photoemission Spectroscopy (MPES)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Jupyter notebook displaying parsing from FHI preprocessing software output (x-array based .h5) to NXmpes formatted nexus" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step -1:** Create a new virtual environment and set up dependencies for jupyterlab_h5web.
This section **should only be run if you do not have Jupyter Lab, its extensions and the extra needed packages.**
For use within the Nomad UI this section should be skipped.
These cells can be run in a Jupyter notebook or copied to a terminal without the \"!\"." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Run the following to start with a fresh virtualenv in **your terminal** in which you are installing and then running **Jupyter lab** if you wish to:
\n", - "```pip install virtualenv && virtualenv --python=python3.7 .nexusenv && source .nexusenv/bin/activate```" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Install jupyter, jupyter-lab and h5web extensions." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! pip install --upgrade nodejs && pip install ipywidgets h5py==3.5.0 h5glance==0.7 h5grove==0.0.14 jupyterlab[full]==3.2.9 jupyterlab_h5web[full]==1.3.0 punx==0.2.5 nexpy==0.14.1 silx[full]==1.0.0 && jupyter lab build" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Enable the extensions" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! jupyter nbextension enable --py widgetsnbextension" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "! jupyter serverextension enable jupyterlab_h5web" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step 0:** Installing and testing nomad-parser-nexus module.
This section **should only be run if you are not running this within NOMAD.** " - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Install nomad and its dependencies. Do not run the following cell if you have a nomad installation running. " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "! pip install --upgrade pip && pip install nomad-lab==1.0.0 --extra-index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple\n", - "! pip list" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Install the nexusparser and its requirements" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! git clone https://github.com/nomad-coe/nomad-parser-nexus.git --recursive && cd nomad-parser-nexus && git status && pip install -r requirements.txt && pip install -e .[all]" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The following cell restarts the kernel after the nexusparser installation" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import os\n", - "os._exit(00)" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step 1:** Download example data (for mpes)" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "Check dependencies of nomad and of the nexusparser and prints them. If the nexusparser and nomad-lab are installed, you are ready to go.
Check if jupyterlab_h5web server and lab extensions are enabled and OK. " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! pip list | grep 'nomad\\|nexus'\n", - "! jupyter serverextension list\n", - "! jupyter labextension list" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Download mpes example data from Zenodo" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "! curl -o MoTe_xarray_final.h5 https://zenodo.org/record/5913599/files/MoTe_xarray_final.h5?download=1" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step 2:** Run your mpes-specific parser on the example data" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Set the nexusparser directory." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import os\n", - "import nexusparser\n", - "nexus_dir = os.path.dirname(nexusparser.__file__) # where the nexusparser module is located!!!!\n", - "print(nexus_dir)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Now we run our parser. The --reader flag takes the mpes reader (mpes), the --nxdl flag takes the application definition for this technique.
" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "! python \"{nexus_dir}/tools/dataconverter/convert.py\" \\\n", - "--reader mpes \\\n", - "--nxdl NXmpes \\\n", - "--input-file MoTe_xarray_final.h5 \\\n", - "--input-file config_file.json \\\n", - "--input-file ELN_metadata_example.yaml \\\n", - "--output mpes.test.nxs" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### Run the same parser alternatively using a function " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from nexusparser.tools.dataconverter.convert import convert" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "convert(input_file=[\"MoTe_xarray_final.h5\", \"config_file.json\", \"ELN_metadata_example.yaml\"],\n", - " reader='mpes',\n", - " nxdl='NXmpes',\n", - " output='mpes.test.nxs')" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The key take home message is that the command above-specified triggers the automatic creation of the HDF5 file.
\n", - "This *.nxs file, is an HDF5 file." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "tags": [] - }, - "source": [ - "### **Step 3:** Inspect the HDF5/NeXus file apm.test.nxs using H5Web" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from jupyterlab_h5web import H5Web" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "h5_file_name = 'mpes.test.nxs'" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "H5Web(h5_file_name)" - ] - } - ], - "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": "3.7.10" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/tests/dataconverter/README.md b/tests/dataconverter/README.md new file mode 100644 index 000000000..d34997a08 --- /dev/null +++ b/tests/dataconverter/README.md @@ -0,0 +1,4 @@ +This is the place for storing code for tests which probe key functionalities of the generic dataconverter. + +## Contact person in FAIRmat for these tests +Sherjeel Shabih \ No newline at end of file diff --git a/tests/tools/dataconverter/__init__.py b/tests/dataconverter/__init__.py similarity index 100% rename from tests/tools/dataconverter/__init__.py rename to tests/dataconverter/__init__.py diff --git a/tests/tools/dataconverter/test_convert.py b/tests/dataconverter/test_convert.py similarity index 83% rename from tests/tools/dataconverter/test_convert.py rename to tests/dataconverter/test_convert.py index b869ee5e4..7cd7ff5dc 100644 --- a/tests/tools/dataconverter/test_convert.py +++ b/tests/dataconverter/test_convert.py @@ -23,17 +23,15 @@ from click.testing import CliRunner import pytest import h5py -from nomad.datamodel import EntryArchive -from nexusparser.tools import nexus # noqa: E402 -import nexusparser.tools.dataconverter.convert as dataconverter -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader -from nexusparser.parser import NexusParser # noqa: E402 +from nexusutils.nexus import nexus # noqa: E402 +import nexusutils.dataconverter.convert as dataconverter +from nexusutils.dataconverter.readers.base.reader import BaseReader def move_xarray_file_to_tmp(tmp_path): """Moves the xarray file, which is used to test linking into the tmp_path directory.""" test_file_path = os.path.join(os.path.dirname(__file__), - "../../data/tools/dataconverter/readers/mpes") + "../data/dataconverter/readers/mpes") file_util.copy_file(os.path.join(test_file_path, "xarray_saved_small_calibration.h5"), os.path.join(tmp_path, "xarray_saved_small_calibration.h5")) @@ -41,7 +39,7 @@ def move_xarray_file_to_tmp(tmp_path): def restore_xarray_file_from_tmp(tmp_path): """Restores the xarray file from the tmp_path directory.""" test_file_path = os.path.join(os.path.dirname(__file__), - "../../data/tools/dataconverter/readers/mpes") + "../data/dataconverter/readers/mpes") os.remove(os.path.join(test_file_path, "xarray_saved_small_calibration.h5")) file_util.move_file(os.path.join(tmp_path, "xarray_saved_small_calibration.h5"), os.path.join(test_file_path, "xarray_saved_small_calibration.h5")) @@ -116,7 +114,7 @@ def test_links_and_virtual_datasets(tmp_path): move_xarray_file_to_tmp(tmp_path) dirpath = os.path.join(os.path.dirname(__file__), - "../../data/tools/dataconverter/readers/example") + "../data/dataconverter/readers/example") runner = CliRunner() result = runner.invoke(dataconverter.convert_cli, [ "--nxdl", @@ -154,7 +152,7 @@ def test_compression(tmp_path): """A test for the convert CLI to check whether a Dataset object is compressed.""" dirpath = os.path.join(os.path.dirname(__file__), - "../../data/tools/dataconverter/readers/example") + "../data/dataconverter/readers/example") move_xarray_file_to_tmp(tmp_path) @@ -168,7 +166,7 @@ def test_compression(tmp_path): test_nxs = h5py.File(os.path.join(tmp_path, "test_output.h5"), "r") assert 'entry/test_compression/compressed_data' in test_nxs assert isinstance(test_nxs['/entry/test_compression/compressed_data'], h5py.Dataset) - assert test_nxs['/entry/test_compression/compressed_data'].compression is 'gzip' + assert test_nxs['/entry/test_compression/compressed_data'].compression == 'gzip' assert test_nxs['/entry/test_compression/not_to_compress'].compression is None restore_xarray_file_from_tmp(tmp_path) @@ -177,33 +175,26 @@ def test_compression(tmp_path): def test_mpes_writing(tmp_path): """Check if mpes example can be reproduced""" # dataconverter - dirpath = os.path.join(os.path.dirname(__file__), "../../data/tools/dataconverter/readers/mpes") + dirpath = os.path.join(os.path.dirname(__file__), "../data/dataconverter/readers/mpes") dataconverter.convert((os.path.join(dirpath, "xarray_saved_small_calibration.h5"), os.path.join(dirpath, "config_file.json")), "mpes", "NXmpes", os.path.join(tmp_path, "mpes.small_test.nxs"), False, False) # check generated nexus file - example_data = os.path.join(tmp_path, 'mpes.small_test.nxs') - logger = logging.getLogger() + test_data = os.path.join(tmp_path, 'mpes.small_test.nxs') + logger = logging.getLogger(__name__) logger.setLevel(logging.DEBUG) - handler = logging.\ - FileHandler(os.path.join(tmp_path, 'nexus_test.log'), 'w') - handler.setLevel(logging.DEBUG) + handler = logging. \ + FileHandler(os.path.join(tmp_path, 'mpes_test.log'), 'w') formatter = logging.Formatter('%(levelname)s - %(message)s') + handler.setLevel(logging.DEBUG) handler.setFormatter(formatter) logger.addHandler(handler) - nexus_helper = nexus.HandleNexus(logger, [example_data]) + nexus_helper = nexus.HandleNexus(logger, [test_data]) nexus_helper.process_nexus_master_file(None) - with open(os.path.join(tmp_path, 'nexus_test.log'), 'r') as logfile: + with open(os.path.join(tmp_path, 'mpes_test.log'), 'r') as logfile: log = logfile.readlines() with open(os.path.join(dirpath, 'Ref_nexus_mpes.log'), 'r') as logfile: ref_log = logfile.readlines() assert log == ref_log - # parsing to NOMAD - archive = EntryArchive() - import structlog - NexusParser().parse(example_data, archive, structlog.get_logger()) - assert archive.nexus.nx_application_mpes.\ - nx_group_ENTRY[0].nx_group_PROCESS[0].nx_group_energy_calibration.\ - nx_field_calibrated_axis.nx_value[0] == pytest.approx(-14.264604, rel=1e-6) diff --git a/tests/tools/dataconverter/test_helpers.py b/tests/dataconverter/test_helpers.py similarity index 96% rename from tests/tools/dataconverter/test_helpers.py rename to tests/dataconverter/test_helpers.py index d6b648c2a..0d55eb3a1 100644 --- a/tests/tools/dataconverter/test_helpers.py +++ b/tests/dataconverter/test_helpers.py @@ -23,8 +23,8 @@ import pytest import numpy as np -import nexusparser.tools.dataconverter.helpers as helpers -from nexusparser.tools.dataconverter.template import Template +import nexusutils.dataconverter.helpers as helpers +from nexusutils.dataconverter.template import Template def alter_dict(data_dict: Template, key: str, value: object): @@ -62,14 +62,14 @@ def listify_template(data_dict: Template): @pytest.fixture(name="nxdl_root") def fixture_nxdl_root(): """pytest fixture to load the same NXDL file for all tests.""" - nxdl_file = os.path.join("tests", "data", "tools", "dataconverter", "NXtest.nxdl.xml") + nxdl_file = os.path.join("tests", "data", "dataconverter", "NXtest.nxdl.xml") yield ET.parse(nxdl_file).getroot() @pytest.fixture(name="template") def fixture_template(): """pytest fixture to use the same template in all tests""" - nxdl_root = ET.parse("tests/data/tools/dataconverter/NXtest.nxdl.xml").getroot() + nxdl_root = ET.parse("tests/data/dataconverter/NXtest.nxdl.xml").getroot() template = Template() helpers.generate_template_from_nxdl(nxdl_root, template) yield template @@ -84,8 +84,8 @@ def fixture_filled_test_data(template, tmp_path): # because h5py.ExternalLink is modifying it while # linking the nxs file. file_util.copy_file(f"{os.path.dirname(__file__)}" - f"/../../" - f"data/tools/dataconverter/" + f"/../" + f"data/dataconverter/" f"readers/mpes/" f"xarray_saved_small_cali" "bration.h5", tmp_path) @@ -138,7 +138,7 @@ def fixture_filled_test_data(template, tmp_path): TEMPLATE["required"]["/ENTRY[my_entry]/NXODD_name/date_value"] = "2022-01-22T12:14:12.05018+00:00" # pylint: disable=E1126 TEMPLATE["optional"]["/ENTRY[my_entry]/required_group/description"] = "An example description" TEMPLATE["optional"]["/ENTRY[my_entry]/required_group2/description"] = "An example description" -TEMPLATE["optional_parents"].append("/ENTRY[entry]/optional_parent") +# TEMPLATE["optional_parents"].append("/ENTRY[entry]/optional_parent") @pytest.mark.parametrize("data_dict,error_message", [ diff --git a/tests/tools/dataconverter/test_readers.py b/tests/dataconverter/test_readers.py similarity index 89% rename from tests/tools/dataconverter/test_readers.py rename to tests/dataconverter/test_readers.py index 6b8d10b53..8178f0eb9 100644 --- a/tests/tools/dataconverter/test_readers.py +++ b/tests/dataconverter/test_readers.py @@ -24,12 +24,12 @@ import pytest -from nexusparser.tools.dataconverter.readers.base.reader import BaseReader -from nexusparser.tools.dataconverter.convert import \ +from nexusutils.dataconverter.readers.base.reader import BaseReader +from nexusutils.dataconverter.convert import \ get_names_of_all_readers, get_reader -from nexusparser.tools.dataconverter.helpers import \ +from nexusutils.dataconverter.helpers import \ validate_data_dict, generate_template_from_nxdl -from nexusparser.tools.dataconverter.template import Template +from nexusutils.dataconverter.template import Template def get_reader_name_from_reader_object(reader) -> str: @@ -43,7 +43,7 @@ def get_reader_name_from_reader_object(reader) -> str: def get_readers_file_names() -> List[str]: """Helper function to parametrize paths of all the reader Python files""" - return glob.glob("nexusparser/tools/dataconverter/readers/*/reader.py") + return glob.glob("nexusutils/dataconverter/readers/*/reader.py") def get_all_readers() -> List[BaseReader]: @@ -78,8 +78,8 @@ def test_has_correct_read_func(reader): reader_name = get_reader_name_from_reader_object(reader) - def_dir = os.path.join(os.getcwd(), "nexusparser", "definitions") - dataconverter_data_dir = os.path.join("tests", "data", "tools", "dataconverter") + def_dir = os.path.join(os.getcwd(), "nexusutils", "definitions") + dataconverter_data_dir = os.path.join("tests", "data", "dataconverter") input_files = glob.glob(os.path.join(dataconverter_data_dir, "readers", reader_name, "*")) for supported_nxdl in reader.supported_nxdls: diff --git a/tests/tools/dataconverter/test_template.py b/tests/dataconverter/test_template.py similarity index 100% rename from tests/tools/dataconverter/test_template.py rename to tests/dataconverter/test_template.py diff --git a/tests/tools/dataconverter/test_writer.py b/tests/dataconverter/test_writer.py similarity index 93% rename from tests/tools/dataconverter/test_writer.py rename to tests/dataconverter/test_writer.py index d078a87f6..d690b0e51 100644 --- a/tests/tools/dataconverter/test_writer.py +++ b/tests/dataconverter/test_writer.py @@ -22,7 +22,7 @@ import pytest import h5py -from nexusparser.tools.dataconverter.writer import Writer +from nexusutils.dataconverter.writer import Writer from .test_helpers import fixture_filled_test_data, fixture_template # pylint: disable=unused-import @@ -32,7 +32,7 @@ def fixture_writer(filled_test_data, tmp_path): """pytest fixture to setup Writer object to be used by tests with dummy data.""" writer = Writer( filled_test_data, - os.path.join("tests", "data", "tools", "dataconverter", "NXtest.nxdl.xml"), + os.path.join("tests", "data", "dataconverter", "NXtest.nxdl.xml"), os.path.join(tmp_path, "test.nxs") ) yield writer diff --git a/tests/nexus/README.md b/tests/nexus/README.md new file mode 100644 index 000000000..37118b3b9 --- /dev/null +++ b/tests/nexus/README.md @@ -0,0 +1,9 @@ +This is the place for storing code for tests which probe key functionalities of the nexus(checker). +Nexuschecker is a core package of which implements functionalities for traversing the XML tree +that is behind the hierarchical data model of NeXus. The nexuschecker `nexus.py` can also be used +as a standalone tool to check how an instance of a NeXus/HDF5 file compares to a given application definition. + +Sandor, please reactivate here your checker code from the master branch and maybe add a small description here. + +## Contact person in FAIRmat for these tests +Sándor Brockhauser \ No newline at end of file diff --git a/nexusparser/__main__.py b/tests/nexus/__init__.py similarity index 60% rename from nexusparser/__main__.py rename to tests/nexus/__init__.py index 21be907a8..db96892bc 100644 --- a/nexusparser/__main__.py +++ b/tests/nexus/__init__.py @@ -1,6 +1,3 @@ -"""main file of tools module - -""" # # Copyright The NOMAD Authors. # @@ -18,18 +15,3 @@ # See the License for the specific language governing permissions and # limitations under the License. # - -import sys -import json -import logging - -from nomad.utils import configure_logging -from nomad.datamodel import EntryArchive -from nexusparser.parser import NexusParser - - -if __name__ == "__main__": - configure_logging(console_log_level=logging.DEBUG) - ARCHIVE = EntryArchive() - NexusParser().parse(sys.argv[1], ARCHIVE, logging) - json.dump(ARCHIVE.m_to_dict(), sys.stdout, indent=2) diff --git a/tests/nexus/test_nexus.py b/tests/nexus/test_nexus.py new file mode 100644 index 000000000..4e1ec9aa0 --- /dev/null +++ b/tests/nexus/test_nexus.py @@ -0,0 +1,94 @@ +"""This is a code that performs several tests on nexus tool + +""" +# +# 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. +# + +import os +import logging +import xml.etree.ElementTree as ET + +from nexusutils.nexus import nexus + + +def test_get_nexus_classes_units_attributes(): + """Check the correct parsing of a separate list for: +Nexus classes (base_classes) +Nexus units (memberTypes) +Nexus attribute type (primitiveTypes) +the tested functions can be found in nexus.py file +""" + + # Test 1 + nexus_classes_list = nexus.get_nx_classes() + + assert 'NXbeam' in nexus_classes_list + + # Test 2 + nexus_units_list = nexus.get_nx_units() + assert 'NX_TEMPERATURE' in nexus_units_list + + # Test 3 + nexus_attribute_list = nexus.get_nx_attribute_type() + assert 'NX_FLOAT' in nexus_attribute_list + + +def test_nexus(tmp_path): + """The nexus test function + +""" + local_dir = os.path.abspath(os.path.dirname(__file__)) + example_data = os.path.join(local_dir, '../data/nexus/201805_WSe2_arpes.nxs') + logger = logging.getLogger(__name__) + logger.setLevel(logging.DEBUG) + handler = logging.\ + FileHandler(os.path.join(tmp_path, 'nexus_test.log'), 'w') + handler.setLevel(logging.DEBUG) + formatter = logging.Formatter('%(levelname)s - %(message)s') + handler.setFormatter(formatter) + logger.addHandler(handler) + nexus_helper = nexus.HandleNexus(logger, [example_data]) + nexus_helper.process_nexus_master_file(None) + + with open(os.path.join(tmp_path, 'nexus_test.log'), 'r') as logfile: + log = logfile.readlines() + with open(os.path.join(local_dir, '../data/nexus/Ref_nexus_test.log'), 'r') as reffile: + ref = reffile.readlines() + + assert log == ref + + # didn't work with filecmp library + # log = os.path.join(local_dir, 'data/nexus_test_data/nexus_test.log') + # ref = os.path.join(local_dir, 'data/nexus_test_data/Ref2_nexus_test.log') + # print('yoyo', filecmp.cmp(log, ref, shallow=False)) + + # print('Testing of nexus.py is SUCCESSFUL.') + + +def test_get_node_at_nxdl_path(): + """Test to verify if we receive the right XML element for a given NXDL path""" + local_dir = os.path.abspath(os.path.dirname(__file__)) + nxdl_file_path = os.path.join(local_dir, "../data/dataconverter/NXtest.nxdl.xml") + elem = ET.parse(nxdl_file_path).getroot() + node = nexus.get_node_at_nxdl_path("/ENTRY/NXODD_name", elem=elem) + assert node.attrib["type"] == "NXdata" + assert node.attrib["name"] == "NXODD_name" + + node = nexus.get_node_at_nxdl_path("/ENTRY/NXODD_name/float_value", elem=elem) + assert node.attrib["type"] == "NX_FLOAT" + assert node.attrib["name"] == "float_value" diff --git a/tests/nyaml2nxdl/README.md b/tests/nyaml2nxdl/README.md new file mode 100644 index 000000000..65de76318 --- /dev/null +++ b/tests/nyaml2nxdl/README.md @@ -0,0 +1,4 @@ +This is the place for storing code for tests of the yaml2nxdl and nxdl2yaml NeXus schema translation routines. + +## Contact person in FAIRmat for these tests +Andrea Albino \ No newline at end of file diff --git a/tests/tools/yaml2nxdl/test_yml2nxdl.py b/tests/nyaml2nxdl/test_nyaml2nxdl.py similarity index 61% rename from tests/tools/yaml2nxdl/test_yml2nxdl.py rename to tests/nyaml2nxdl/test_nyaml2nxdl.py index a1037e3b9..bdb7b0625 100755 --- a/tests/tools/yaml2nxdl/test_yml2nxdl.py +++ b/tests/nyaml2nxdl/test_nyaml2nxdl.py @@ -28,13 +28,8 @@ import xml.etree.ElementTree as ET import pytest from click.testing import CliRunner -import nexusparser.tools.yaml2nxdl.yaml2nxdl as yml2nxdl -from nexusparser.tools.yaml2nxdl import yaml2nxdl_forward_tools - -sys.path.insert(0, '../nexusparser/tools') -sys.path.insert(0, '../nexusparser/tools/yaml2nxdl') - -LOCALDIR = os.path.abspath(os.path.dirname(__file__)) +import nexusutils.nyaml2nxdl.nyaml2nxdl as nyml2nxdl +from nexusutils.nyaml2nxdl import nyaml2nxdl_forward_tools def delete_duplicates(list_of_matching_string): @@ -89,7 +84,7 @@ def compare_matches(ref_xml_file, test_yml_file, test_xml_file, desired_matches) ref_matches = find_matches(ref_xml_file, desired_matches) # Test file is generated runner = CliRunner() - result = runner.invoke(yml2nxdl.launch_tool, ['--input-file', test_yml_file]) + result = runner.invoke(nyml2nxdl.launch_tool, ['--input-file', test_yml_file]) assert result.exit_code == 0 check_file_fresh_baked(test_xml_file) # Test file is read @@ -101,16 +96,16 @@ def test_links(): """Check the correct parsing of links """ - ref_xml_link_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXtest_links.nxdl.xml' - test_yml_link_file = 'tests/data/tools/yaml2nxdl_test_data/NXtest_links.yml' - test_xml_link_file = 'tests/data/tools/yaml2nxdl_test_data/NXtest_links.nxdl.xml' + ref_xml_link_file = 'tests/data/nyaml2nxdl/Ref_NXtest_links.nxdl.xml' + test_yml_link_file = 'tests/data/nyaml2nxdl/NXtest_links.yml' + test_xml_link_file = 'tests/data/nyaml2nxdl/NXtest_links.nxdl.xml' desired_matches = [''] compare_matches( ref_xml_link_file, test_yml_link_file, test_xml_link_file, desired_matches) - os.remove('tests/data/tools/yaml2nxdl_test_data/NXtest_links.nxdl.xml') + os.remove('tests/data/nyaml2nxdl/NXtest_links.nxdl.xml') sys.stdout.write('Test on links okay.\n') @@ -119,16 +114,16 @@ def test_docs(): The xml trees of the two files are then compared. """ - ref_xml_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry-docCheck.nxdl.xml' - test_yml_file = 'tests/data/tools/yaml2nxdl_test_data/NXellipsometry-docCheck.yaml' - test_xml_file = 'tests/data/tools/yaml2nxdl_test_data/NXellipsometry-docCheck.nxdl.xml' + ref_xml_file = 'tests/data/nyaml2nxdl/Ref_NXellipsometry-docCheck.nxdl.xml' + test_yml_file = 'tests/data/nyaml2nxdl/NXellipsometry-docCheck.yaml' + test_xml_file = 'tests/data/nyaml2nxdl/NXellipsometry-docCheck.nxdl.xml' desired_matches = [''] compare_matches( ref_xml_file, test_yml_file, test_xml_file, desired_matches) - os.remove('tests/data/tools/yaml2nxdl_test_data/NXellipsometry-docCheck.nxdl.xml') + os.remove('tests/data/nyaml2nxdl/NXellipsometry-docCheck.nxdl.xml') sys.stdout.write('Test on documentation formatting okay.\n') @@ -137,10 +132,10 @@ def test_nxdl2yaml_doc_format(): to check if they are correct. """ - ref_xml_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXentry.nxdl.xml' - ref_yml_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXentry.yml' - test_yml_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXentry_parsed.yml' - result = CliRunner().invoke(yml2nxdl.launch_tool, ['--input-file', ref_xml_file]) + ref_xml_file = 'tests/data/nyaml2nxdl/Ref_NXentry.nxdl.xml' + ref_yml_file = 'tests/data/nyaml2nxdl/Ref_NXentry.yml' + test_yml_file = 'tests/data/nyaml2nxdl/Ref_NXentry_parsed.yml' + result = CliRunner().invoke(nyml2nxdl.launch_tool, ['--input-file', ref_xml_file]) assert result.exit_code == 0 check_file_fresh_baked(test_yml_file) @@ -155,18 +150,18 @@ def test_fileline_error(): """In this test the yaml fileline in the error message is tested. """ - test_yml_file = 'tests/data/tools/yaml2nxdl_test_data/NXfilelineError1.yml' - result = CliRunner().invoke(yml2nxdl.launch_tool, ['--input-file', test_yml_file]) + test_yml_file = 'tests/data/nyaml2nxdl/NXfilelineError1.yml' + result = CliRunner().invoke(nyml2nxdl.launch_tool, ['--input-file', test_yml_file]) assert result.exit_code == 1 assert '13' in str(result.exception) - test_yml_file = 'tests/data/tools/yaml2nxdl_test_data/NXfilelineError2.yml' - result = CliRunner().invoke(yml2nxdl.launch_tool, ['--input-file', test_yml_file]) + test_yml_file = 'tests/data/nyaml2nxdl/NXfilelineError2.yml' + result = CliRunner().invoke(nyml2nxdl.launch_tool, ['--input-file', test_yml_file]) assert result.exit_code == 1 assert '21' in str(result.exception) - test_yml_file = 'tests/data/tools/yaml2nxdl_test_data/NXfilelineError3.yml' - result = CliRunner().invoke(yml2nxdl.launch_tool, ['--input-file', test_yml_file]) + test_yml_file = 'tests/data/nyaml2nxdl/NXfilelineError3.yml' + result = CliRunner().invoke(nyml2nxdl.launch_tool, ['--input-file', test_yml_file]) assert result.exit_code == 1 assert '25' in str(result.exception) @@ -177,16 +172,16 @@ def test_symbols(): """Check the correct parsing of symbols """ - ref_xml_symbol_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXnested_symbols.nxdl.xml' - test_yml_symbol_file = 'tests/data/tools/yaml2nxdl_test_data/NXnested_symbols.yml' - test_xml_symbol_file = 'tests/data/tools/yaml2nxdl_test_data/NXnested_symbols.nxdl.xml' + ref_xml_symbol_file = 'tests/data/nyaml2nxdl/Ref_NXnested_symbols.nxdl.xml' + test_yml_symbol_file = 'tests/data/nyaml2nxdl/NXnested_symbols.yml' + test_xml_symbol_file = 'tests/data/nyaml2nxdl/NXnested_symbols.nxdl.xml' desired_matches = ['', '', '', '', ''] compare_matches( ref_xml_attribute_file, test_yml_attribute_file, test_xml_attribute_file, desired_matches) - os.remove('tests/data/tools/yaml2nxdl_test_data/NXattributes.nxdl.xml') + os.remove('tests/data/nyaml2nxdl/NXattributes.nxdl.xml') sys.stdout.write('Test on attributes okay.\n') @@ -212,16 +207,16 @@ def test_extends(): """Check the correct handling of extends keyword """ - ref_xml_attribute_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXattributes.nxdl.xml' - test_yml_attribute_file = 'tests/data/tools/yaml2nxdl_test_data/NXattributes.yml' - test_xml_attribute_file = 'tests/data/tools/yaml2nxdl_test_data/NXattributes.nxdl.xml' + ref_xml_attribute_file = 'tests/data/nyaml2nxdl/Ref_NXattributes.nxdl.xml' + test_yml_attribute_file = 'tests/data/nyaml2nxdl/NXattributes.yml' + test_xml_attribute_file = 'tests/data/nyaml2nxdl/NXattributes.nxdl.xml' runner = CliRunner() - result = runner.invoke(yml2nxdl.launch_tool, ['--input-file', test_yml_attribute_file]) + result = runner.invoke(nyml2nxdl.launch_tool, ['--input-file', test_yml_attribute_file]) assert result.exit_code == 0 ref_root_node = ET.parse(ref_xml_attribute_file).getroot() test_root_node = ET.parse(test_xml_attribute_file).getroot() assert ref_root_node.attrib == test_root_node.attrib - os.remove('tests/data/tools/yaml2nxdl_test_data/NXattributes.nxdl.xml') + os.remove('tests/data/nyaml2nxdl/NXattributes.nxdl.xml') sys.stdout.write('Test on extends keyword okay.\n') @@ -230,9 +225,9 @@ def test_symbols_and_enum_docs(): or attributes fields, e.g. doc """ - ref_xml_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXmytests.nxdl.xml' - test_yml_file = 'tests/data/tools/yaml2nxdl_test_data/NXmytests.yml' - test_xml_file = 'tests/data/tools/yaml2nxdl_test_data/NXmytests.nxdl.xml' + ref_xml_file = 'tests/data/nyaml2nxdl/Ref_NXmytests.nxdl.xml' + test_yml_file = 'tests/data/nyaml2nxdl/NXmytests.yml' + test_xml_file = 'tests/data/nyaml2nxdl/NXmytests.nxdl.xml' desired_matches = ['', '', '', '', '', '', ' yml -> xml okay.\n') @@ -279,22 +274,22 @@ def test_yml_parsing(): The xml trees of the two files are then compared. """ - ref_yml_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry.yml' - test_xml_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry.nxdl.xml' - test_yml_file = 'tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry_parsed.yml' - result = CliRunner().invoke(yml2nxdl.launch_tool, ['--input-file', ref_yml_file]) + ref_yml_file = 'tests/data/nyaml2nxdl/Ref_NXellipsometry.yml' + test_xml_file = 'tests/data/nyaml2nxdl/Ref_NXellipsometry.nxdl.xml' + test_yml_file = 'tests/data/nyaml2nxdl/Ref_NXellipsometry_parsed.yml' + result = CliRunner().invoke(nyml2nxdl.launch_tool, ['--input-file', ref_yml_file]) assert result.exit_code == 0 check_file_fresh_baked(test_xml_file) - result = CliRunner().invoke(yml2nxdl.launch_tool, ['--input-file', test_xml_file]) + result = CliRunner().invoke(nyml2nxdl.launch_tool, ['--input-file', test_xml_file]) assert result.exit_code == 0 check_file_fresh_baked(test_yml_file) - test_yml_tree = yaml2nxdl_forward_tools.yml_reader(test_yml_file) + test_yml_tree = nyaml2nxdl_forward_tools.yml_reader(test_yml_file) - ref_yml_tree = yaml2nxdl_forward_tools.yml_reader(ref_yml_file) + ref_yml_tree = nyaml2nxdl_forward_tools.yml_reader(ref_yml_file) assert list(test_yml_tree) == list(ref_yml_tree), 'Ref YML and parsed YML \ has not the same root entries!!' - os.remove('tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry_parsed.yml') - os.remove('tests/data/tools/yaml2nxdl_test_data/Ref_NXellipsometry.nxdl.xml') + os.remove('tests/data/nyaml2nxdl/Ref_NXellipsometry_parsed.yml') + os.remove('tests/data/nyaml2nxdl/Ref_NXellipsometry.nxdl.xml') sys.stdout.write('Test on yml -> xml -> yml okay.\n') diff --git a/tests/test_nexus.py b/tests/test_nexus.py deleted file mode 100644 index efb489d25..000000000 --- a/tests/test_nexus.py +++ /dev/null @@ -1,192 +0,0 @@ -"""This is a code that performs several tests on nexus tool - -""" -# -# 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. -# - -from typing import cast, Any -import pytest - -from nomad.metainfo import Definition, MSection, Section -from nomad.datamodel import EntryArchive -from nexusparser.metainfo import nexus -from nexusparser import tools - - -@pytest.mark.parametrize('path,value', [ - pytest.param('APPLICATIONS.name', 'nexus'), - pytest.param('APPLICATIONS.NXobject.name', 'NXobject'), - pytest.param('APPLICATIONS.NXentry.nx_kind', 'group'), - pytest.param('APPLICATIONS.NXentry.defaultAttribute.nx_value.type', str), - pytest.param('APPLICATIONS.NXentry.nx_attribute_default', '*'), - pytest.param('APPLICATIONS.NXentry.NXdataGroup', '*'), - pytest.param('APPLICATIONS.NXdetector.real_timeField', '*'), - pytest.param('APPLICATIONS.NXentry.NXdataGroup.nx_optional', True), - pytest.param('APPLICATIONS.NXentry.nx_group_DATA.section_def.nx_kind', 'group'), - pytest.param('APPLICATIONS.NXentry.nx_group_DATA.section_def.nx_optional', True), - pytest.param('APPLICATIONS.NXentry.nx_group_DATA.section_def.nx_name.type', str), - pytest.param('APPLICATIONS.NXdetector.real_timeField.name', 'real_timeField'), - pytest.param('APPLICATIONS.NXdetector.real_timeField.nx_type', 'NX_NUMBER'), - pytest.param('APPLICATIONS.NXdetector.real_timeField.nx_units', 'NX_TIME'), - pytest.param('APPLICATIONS.NXdetector.real_timeField.nx_unit', '*'), - pytest.param('APPLICATIONS.NXdetector.real_timeField.nx_value', '*'), - pytest.param('APPLICATIONS.NXarpes.NXentryGroup.NXdataGroup.nx_optional', False), - pytest.param('APPLICATIONS.NXentry.nx_category', 'base'), - pytest.param('APPLICATIONS.NXapm.nx_category', 'application') -]) -def test_assert_nexus_metainfo(path: str, value: Any): - """Test the existance of nexus metainfo - -""" - segments = path.split('.') - package, definition_names = segments[0], segments[1:] - - current: Definition = getattr(nexus, package) - for name in definition_names: - for content in current.m_contents(): - if getattr(content, 'name', None) == name: - current = cast(Definition, content) - break - - else: - current = getattr(current, name, None) - - if current is None: - assert False, f'{path} does not exist' - - if value == '*': - assert current is not None, f'{path} does not exist' - elif value is None: - assert current is None, f'{path} does exist' - else: - assert current == value, f'{path} has wrong value' - - if isinstance(current, Section): - assert current.nx_kind is not None - for base_section in current.all_base_sections: - assert base_section.nx_kind == current.nx_kind - - -def test_use_nexus_metainfo(): - """Test on use of Nexus metainfo - -""" - # pylint: disable=no-member - archive = EntryArchive() - archive.nexus = nexus.Nexus() - archive.nexus.nx_application_arpes = nexus.NXarpes() - archive.nexus.nx_application_arpes.m_create(nexus.NXarpes.NXentryGroup) - archive.nexus.nx_application_arpes.nx_group_ENTRY[0].nx_field_title = \ - nexus.NXarpes.NXentryGroup.titleField() - archive.nexus.nx_application_arpes.nx_group_ENTRY[0].nx_field_title.nx_value = 'my title' - - # Entry/default is not overwritten in NXarpes. Therefore technically, - # there is no attribute section - # nexus.NXarpes.NXentryGroup.DefaultAttribute. We artifically extented inheritence to - # include inner section/classes. So both options work: - # archive.nexus.nx_application_arpes.nx_group_ENTRY.nx_attribute_default = - # nexus.NXentry.DefaultAttribute() - archive.nexus.nx_application_arpes.nx_group_ENTRY[0].nx_attribute_default = \ - nexus.NXarpes.NXentryGroup.defaultAttribute() - archive.nexus.nx_application_arpes.nx_group_ENTRY[0].nx_attribute_default.nx_value = \ - 'my default' - # pylint: enable=no-member - - archive = EntryArchive.m_from_dict(archive.m_to_dict()) - assert archive.nexus.nx_application_arpes.nx_group_ENTRY[0].nx_attribute_default.nx_value == \ - 'my default' - assert archive.nexus.nx_application_arpes.nx_group_ENTRY[0].nx_field_title.nx_value == \ - 'my title' - - -@pytest.mark.parametrize('path', [ - pytest.param('NXarpes:app/NXentry:group/title:field/my title:value', id='field'), - pytest.param('NXarpes:app/NXentry:group/default:attribute/my default:value', id='attribute') -]) -def test_use_nexus_metainfo_reflectivly(path): - """Test of the use of nexus metainfo reflectivly - -""" - archive = EntryArchive() - archive.nexus = nexus.Nexus() # pylint: disable=no-member - parent_object: MSection = archive.nexus - parent_definition: Section = nexus.Nexus.m_def # pylint: disable=no-member - - segments = path.split('/') - for segment in segments: - name_or_value, kind = segment.split(':') - if kind in ['app', 'group', 'field', 'attribute']: - if kind == 'app': - section_definition = nexus.APPLICATIONS.all_definitions[name_or_value] - sub_section_definition = \ - parent_definition.all_sub_sections[name_or_value.replace('NX', '\ -nx_application_')] - - if kind == 'group': - section_definition = \ - parent_definition.all_inner_section_definitions[f'{name_or_value}Group'] - sub_section_definition = \ - parent_definition.all_sub_sections[f'nx_group_' - f'{name_or_value.replace("NX", "").upper()}' - ] - - if kind == 'field': - section_definition = \ - parent_definition.all_inner_section_definitions[f'{name_or_value}Field'] - sub_section_definition = \ - parent_definition.all_sub_sections[f'nx_field_{name_or_value}'] - - if kind == 'attribute': - section_definition = \ - parent_definition.all_inner_section_definitions[f'{name_or_value}Attribute'] - sub_section_definition = \ - parent_definition.all_sub_sections[f'nx_attribute_{name_or_value}'] - - new_object = section_definition.section_cls() - parent_object.m_add_sub_section(sub_section_definition, new_object) - - elif kind == 'value': - parent_object.m_set(parent_definition.all_quantities['nx_value'], name_or_value) - - else: - assert False, 'kind does not exist' - - parent_object = new_object - parent_definition = section_definition - - -def test_get_nexus_classes_units_attributes(): - """Check the correct parsing of a separate list for: -Nexus classes (base_classes) -Nexus units (memberTypes) -Nexus attribute type (primitiveTypes) -the tested functions can be found in nexus.py file -""" - - # Test 1 - nexus_classes_list = tools.nexus.get_nx_classes() - - assert 'NXbeam' in nexus_classes_list - - # Test 2 - nexus_units_list = tools.nexus.get_nx_units() - assert 'NX_TEMPERATURE' in nexus_units_list - - # Test 3 - nexus_attribute_list = tools.nexus.get_nx_attribute_type() - assert 'NX_FLOAT' in nexus_attribute_list diff --git a/tests/test_parser.py b/tests/test_parser.py deleted file mode 100644 index 4791550f2..000000000 --- a/tests/test_parser.py +++ /dev/null @@ -1,160 +0,0 @@ -"""Test scripts for parser.py tool - -""" -# -# 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. -# - -import xml.etree.ElementTree as ET -import sys -import os -import logging -import pytest -from nomad.datamodel import EntryArchive -from nexusparser.tools import nexus # noqa: E402 -from nexusparser.parser import NexusParser # noqa: E402 -sys.path.insert(0, '.') -sys.path.insert(0, '..') -sys.path.insert(0, '../..') - - -@pytest.fixture(name="parser") -def fixture_parser(): - """Helper function to launch NexusParser class - -""" - yield NexusParser() - - -def test_nexus(tmp_path): - """The nexus test function - -""" - local_dir = os.path.abspath(os.path.dirname(__file__)) - example_data = os.path.join(local_dir, 'data/nexus_test_data/201805_WSe2_arpes.nxs') - logger = logging.getLogger() - logger.setLevel(logging.DEBUG) - handler = logging.\ - FileHandler(os.path.join(tmp_path, 'nexus_test.log'), 'w') - handler.setLevel(logging.DEBUG) - formatter = logging.Formatter('%(levelname)s - %(message)s') - handler.setFormatter(formatter) - logger.addHandler(handler) - nexus_helper = nexus.HandleNexus(logger, [example_data]) - nexus_helper.process_nexus_master_file(None) - - with open(os.path.join(tmp_path, 'nexus_test.log'), 'r') as logfile: - log = logfile.readlines() - with open(os.path.join(local_dir, 'data/nexus_test_data/Ref_nexus_test.log'), 'r') as reffile: - ref = reffile.readlines() - - assert log == ref - - # didn't work with filecmp library - # log = os.path.join(local_dir, 'data/nexus_test_data/nexus_test.log') - # ref = os.path.join(local_dir, 'data/nexus_test_data/Ref2_nexus_test.log') - # print('yoyo', filecmp.cmp(log, ref, shallow=False)) - - print('Testing of nexus.py is SUCCESSFUL.') - - -def test_get_node_at_nxdl_path(): - """Test to verify if we receive the right XML element for a given NXDL path""" - nxdl_file_path = "tests/data/tools/dataconverter/NXtest.nxdl.xml" - elem = ET.parse(nxdl_file_path).getroot() - node = nexus.get_node_at_nxdl_path("/ENTRY/NXODD_name", elem=elem) - assert node.attrib["type"] == "NXdata" - assert node.attrib["name"] == "NXODD_name" - - node = nexus.get_node_at_nxdl_path("/ENTRY/NXODD_name/float_value", elem=elem) - assert node.attrib["type"] == "NX_FLOAT" - assert node.attrib["name"] == "float_value" - - -def test_example(parser): - """Tests if parser can parse our example data - -""" - archive = EntryArchive() - - import structlog - - # local_dir = os.path.abspath(os.path.dirname(__file__)) - # example_data = os.path.join(local_dir, 'data/nexus_test_data/em0001.test.nxs') - # parser().parse(example_data, archive, structlog.get_logger()) - # assert archive.nexus.nx_application_em_nion.\ - # nx_group_ENTRY[0].nx_group_operator.nx_field_affiliation.nx_value == - # "Humboldt Universität zu Berlin" - - # local_dir = os.path.abspath(os.path.dirname(__file__)) - # example_data = os.path.join(local_dir, 'data/nexus_test_data/mpes2.test.nxs') - # parser().parse(example_data, archive, structlog.get_logger()) - # assert archive.nexus.nx_application_mpes.\ - # nx_group_ENTRY[0].nx_field_definition.nx_value == "NXmpes" - - local_dir = os.path.abspath(os.path.dirname(__file__)) - example_data = os.path.join(local_dir, 'data/nexus_test_data/201805_WSe2_arpes.nxs') - parser.parse(example_data, archive, structlog.get_logger()) - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_SAMPLE[0].nx_field_pressure.nx_value == 3.27e-10 - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_SAMPLE[0].nx_field_pressure.nx_unit == "millibar" - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_SAMPLE[0].nx_field_pressure.m_def.nx_units == "NX_PRESSURE" - assert archive.nexus.nx_application_arpes.nx_group_ENTRY[0].nx_group_INSTRUMENT[0].\ - nx_group_monochromator.nx_field_energy.nx_value == 36.49699020385742 - assert archive.nexus.nx_application_arpes.nx_group_ENTRY[0].nx_group_INSTRUMENT[0].\ - nx_group_monochromator.nx_field_energy.nx_name == 'energy' - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_INSTRUMENT[0].nx_group_analyser.\ - nx_field_entrance_slit_size.nx_value == 750 - # good ENUM - x-ray - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_INSTRUMENT[0].nx_group_SOURCE[0].\ - nx_field_probe.nx_value == 'x-ray' - # wrong inherited ENUM - Burst - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_INSTRUMENT[0].nx_group_SOURCE[0].\ - nx_field_mode.nx_value is None - # wrong inherited ENUM for extended field - 'Free Electron Laser' - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_INSTRUMENT[0].nx_group_SOURCE[0].\ - nx_field_type.nx_value is None - # 1D datasets - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_VARIABLE[0].nx_name == "angles" - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_VARIABLE[1].nx_name == "delays" - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_VARIABLE[2].nx_name == "energies" - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_VARIABLE[0].nx_unit == "1/Å" - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_VARIABLE[1].nx_unit == "fs" - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_VARIABLE[2].nx_unit == "eV" - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_VARIABLE[0].nx_value[0] == 0.10033616393632831 - # 2D datasets - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_DATA[0].nx_name == "data" - assert archive.nexus.nx_application_arpes.\ - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_DATA[0].nx_value[2] == 0.0 - assert pytest.approx( - archive.nexus.nx_application_arpes. - nx_group_ENTRY[0].nx_group_DATA[0].nx_field_DATA[0].nx_value[3] - 0.00078192557) \ - == 0.0