emanuele/eXParser-PLD
SHA256
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 2 Wiki Activity

new docs, up to installation procedure

Browse Source
This commit is contained in:
Emanuele D'Amico
2026-05-14 01:40:54 +02:00
parent 50a1ba9f22
commit dc916b1207
5 changed files with 77 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
docs/user-manual_intro.adoc
View File

@@ -1,8 +1,8 @@
== Introduction
// TO-DO: Grammar-check. I'm totally fried right now and can't seem to complete even a single proper
*eXParser* - short for _**e**LabFTW to Ne**X**us **Parser**_ - is (hopefully) a family of specialized parsing software applications, mainly developed in Python, whose primary job is to automatically transform experimental metadata and data - originally stored as JSON objects inside an electronic lab notebook - into standardized, self-descriptive **NeXus files**.
*{software-family}* - short for _**e**LabFTW to Ne**X**us **Pars**er_ - is (hopefully) a family of specialized parsing software applications, mainly developed in Python, whose primary job is to automatically transform experimental metadata and data - originally stored as JSON objects inside an electronic lab notebook - into standardized, self-descriptive **NeXus files**.
The software is designed to fetch "scattered" data (often distributed across multiple linked entries) from our eLNfootnote:[Acronym for "_electronic Lab Notebook_".] of choice - link:{elabftw-site}[**eLabFTW**^] - where the data is originally stored as JSON objects. It then parses the included metadata to resolve the full dataset which is then used to create a dictionary following a pre-established schema (dependent on the analysis or fabrication method, e.g., PLD, XRD, or RHEED), and finally uses said dictionary to produce an **HDF5/NeXus File** which complies with the **FAIR Principles** and the guidelines given within the context of the Italian PNRRfootnote:pnrr[PNRR stands for _National Recovery and Resilience Plan_.] **NFFA-DI**.
The software is designed to fetch "scattered" data (often distributed across multiple linked entries) from our eLNfootnote:[Acronym for "_electronic Lab Notebook_".] of choice - link:{elabftw-site}[**eLabFTW**^] - where the data is originally stored as JSON objects. It then parses the included metadata to resolve the full dataset which is then used to create a dictionary following a pre-established schema (dependent on the analysis or fabrication method, e.g., PLD, XRD, or RHEED), and finally uses said dictionary to produce an **HDF5/NeXus file** which complies with the **FAIR Principles** and the guidelines given within the context of the Italian PNRRfootnote:pnrr[PNRR stands for _National Recovery and Resilience Plan_.] **NFFA-DI**.
Specifically, *{software-name}* is designed for *Pulsed Laser Deposition / PLD* fabrications.
@@ -35,10 +35,18 @@ Although separated into different database constructs, experiments and items all
// method-specific
In a software like eLabFTW where data can (and will) be spread out through multiple entries, a particularly useful feature is **linking**: the software allows you to link experiments or items with each other, using elabid's as identifiers. For a PLD deposition, you can link the experiment describing a single layer to the target used, the substrate, the PLD instrument and the sample produced itself (all of which are eLabFTW items). This creates a complete provenance graph which can be (not-so) easily resolved starting from the sample's metadata and a chain of HTTP requests.
In this optic, {software-name} interacts with eLabFTW via its REST API (Application Programming Interface). It reads a starting sample's ID (the entrypoint), fetches the relevant JSON metadata, chains requests using the elabid's of the sample's linked resources and experiments, rebuilds the entire dataset and if available downloads attached instrument files (e.g., RHEED intensities, images) to package all of it into the final NeXus file.
In this optic, {software-name} interacts with eLabFTW via its REST API (Application Programming Interface). It reads a starting sample's ID (the entry point), fetches the relevant JSON metadata, chains requests using the elabid's of the sample's linked resources and experiments, rebuilds the entire dataset and if available downloads attached instrument files (e.g., RHEED intensities, images) to package all of it into the final NeXus file.
=== HDF5 and NeXus Files
=== The output: HDF5 and NeXus files
The output of {software-family} is an **HDF5 (Hierarchical Data Format ver. 5) file**, which is a powerful file format designed to store and organize large volumes of numerical data. It acts like a virtual file system inside a single file, using a hierarchical group/dataset structures in the same way a file system uses folders and files - with both elements having their own metadata; this way the file is self-describing, containing all relevant information like a small database. HDF5 also supports efficient slicing, compression and parallel I/O. The file extension of such format is `.h5`.
== Using the software
On the other hand, *NeXus* is a common data standard [.underline]#built on top of HDF5#. It defines fixed conventions for naming groups, datasets and attributes, specifically for neutron, X-ray, and now materials science experiments. NeXus provides "application definitions" (like _NXpld_fabrication_ for PLD) that specify exactly which fields must/may appear. NeXus is also heavily promoted by _FAIRmat_, a German-based consortium, part of the NFDI, whose main mission is providing scientists «with a FAIR data infrastructure and the skills and tool they need to make the most of it»footnote:[As stated on their link:{fairmat-site}[website^].]. The file extension of such format is `.nxs`, but generally file viewers treat the two formats similarly.
== Troubleshooting
Last but not least, NeXus is also the format of choice for data sharing in the NFFA-DI guidelines. Which brings us to the reason why {software-family} exists.
==== Reading HDF5/NeXus files
While writing an HDF5/NeXus file usually requires dedicated software and/or a good knowledge of programming and familiarity with specific libraries (like h5py), there are multiple ways to read these files even without such knowledge.
One of such ways would be using the online NeXus file viewer of the NCNR (_NIST Center for Neutron Research_), available on their link:{ncnr-viewer}[website^]. The "_Browse..._" button at the bottom allows for uploading both h5 and nxs files, although drag and drop also works.
Another similar but in my opinion more elegant online file viewer is the one hosted by the HDF5 Group: link:{hdf5-viewer}[MyHDF5^]. Other than the more modern appearance this viewer doesn't upload files to any remote server, with every operation happening locally in your browser; the drag and drop works better meaning you won't accidentally reload the page if you miss the dropping area, and the viewer also allows for opening multiple concurrent files, and downloading h5 files from URL.