From c7fa0c144c39423fbbe805b92dc85bd704986467 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Wed, 9 Oct 2024 16:16:56 +0200 Subject: [PATCH 1/3] fix link in docs --- docs/tutorial/converting-data-to-nexus.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorial/converting-data-to-nexus.md b/docs/tutorial/converting-data-to-nexus.md index 1558562f1..5c5510503 100644 --- a/docs/tutorial/converting-data-to-nexus.md +++ b/docs/tutorial/converting-data-to-nexus.md @@ -27,7 +27,7 @@ We will use the [XPS reader plugin](https://github.com/FAIRmat-NFDI/pynxtools-xp #### Steps -1. Download the example files from here: [Example files](https://download-directory.github.io/?url=https://github.com/FAIRmat-NFDI/pynxtools-xps/tree/main/examples/sle) +1. Download the example files from here: [Example files](https://download-directory.github.io/?url=https://github.com/FAIRmat-NFDI/pynxtools-xps/tree/main/examples/specs/sle) 2. **Extract** the zip and copy the files in your current working directory. You can find the working directory by typing the following in your terminal: ```console pwd From 6a57a61fe025e2c3266203a331f64e96ddd3d431 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Thu, 10 Oct 2024 10:23:49 +0200 Subject: [PATCH 2/3] remove mpes and sts example README --- examples/README.md | 24 +++++++++--------------- examples/mpes/README.md | 35 ----------------------------------- examples/sts/README.md | 32 -------------------------------- 3 files changed, 9 insertions(+), 82 deletions(-) delete mode 100644 examples/mpes/README.md delete mode 100644 examples/sts/README.md diff --git a/examples/README.md b/examples/README.md index f9ba28974..6ff784932 100644 --- a/examples/README.md +++ b/examples/README.md @@ -1,20 +1,14 @@ ## Getting started -We offer examples of how you can convert your data (raw data, numerical data, metadata), +Here, we provide examples of how you can convert your data (raw data, numerical data, metadata), from your acquisition software or electronic lab notebook (ELN), into a NeXus/HDF5 file -using the [dataconverter](../pynxtools/dataconverter) tool. -This tool offers parsers/readers/data extractors for various experimental techniques via -technique specific plugins. +using the [built-in readers of pynxtools](https://fairmat-nfdi.github.io/pynxtools/reference/built-in-readers.html). -The examples contain code snippets for creating a NeXus/HDF5 file for the experimental technique -according to a standardized NeXus application definition (e.g. NXem, NXmpes, NXellipsometry, -NXapm, NXopt, NXxps, NXraman). -Respective [Jupyter Notebooks](https://jupyter.org/) are used for running these examples. +There is also [documentation](https://fairmat-nfdi.github.io/pynxtools/learn/dataconverter-and-readers.html) of the [dataconverter](../pynxtools/dataconverter) available. You can write a [reader](../pynxtools/dataconverter/readers) for your experimental technique +if it is not supported yet, see documentation [here](https://fairmat-nfdi.github.io/pynxtools/how-tos/build-a-plugin.html). -There is also a documentation of the [dataconverter](../pynxtools/dataconverter) available. -You can also write a [reader](../pynxtools/dataconverter/readers) for your experimental technique -if it is not supported yet. Feel also free to [contact](../README.md#questions-suggestions) -us if you need help. - -For giving specific feedback to specific parsers/readers/data extractors please contact the -respective developers directly and checkout the domain-specific pynxtools plugins: +Note that `pynxtools` offers a number of FAIRmat-supported parsers/readers/data extractors for various experimental techniques via +technique specific plugins. You can find the list [here](https://fairmat-nfdi.github.io/pynxtools/reference/plugins.html). You can find +examples for using each of them in the individual repositories and in their documentation. +For giving feedback to specific parsers/readers/data extractors, please checkout the domain-specific `pynxtools` plugins and their examples +or contact the respective developers directly. diff --git a/examples/mpes/README.md b/examples/mpes/README.md deleted file mode 100644 index 2fe4d27a1..000000000 --- a/examples/mpes/README.md +++ /dev/null @@ -1,35 +0,0 @@ -# What is MPES? - -The [NXmpes](https://fairmat-experimental.github.io/nexus-fairmat-proposal/9636feecb79bb32b828b1a9804269573256d7696/classes/contributed_definitions/NXmpes.html#nxmpes) application definition is an umbrella definition for all photo-emission related techniques, such as ARPES or XPS. - -# How to use it? - -This is an example to use the dataconvert with the `mpes` reader and the `NXmpes` application definition. -If you want to use some example data you can find small example files in [`tests/data/dataconverter/readers/mpes`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/tests/data/dataconverter/readers/mpes). - -```shell -dataconverter --reader mpes \\ - --nxdl NXmpes \\ - xarray_saved_small_calibration \\ - config_file.json \\ - eln_data.yaml \\ - --output mpes_example.nxs -``` - -The reader is a tailored parser for research data in a common format. This particular example is able to read and map hdf5 files, as well as json and yaml files. Feel free to contact FAIRmat if you want to create a parser for your research data. - -For XPS data, you may install the [`pnyxtoools-xps`](https://github.com/FAIRmat-NFDI/pynxtools-xps) plugin and use its [example data in XML format](https://github.com/FAIRmat-NFDI/pynxtools-xps/tree/main/examples/xml) with the command - -```shell -dataconverter --reader xps \\ - --nxdl NXmpes \\ - eln_data.yaml \\ - In-situ_PBTTT_XPS_SPECS.xml \\ - --output xps_example.nxs -``` - -# Are there detailed examples? - -Yes, [here](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/tree/develop/docker/mpes) you can find exhaustive examples how to use `pynxtools` for your ARPES research data pipeline. - -There is also an [example](https://gitlab.mpcdf.mpg.de/nomad-lab/north/xps) for using `pynxtools` and `pnyxtoools-xps` for an XPS pipeline. diff --git a/examples/sts/README.md b/examples/sts/README.md deleted file mode 100644 index 9a0d0409e..000000000 --- a/examples/sts/README.md +++ /dev/null @@ -1,32 +0,0 @@ -# STS Reader -***Note: Though the reader name is STS reader it also supports STM type experiment. This is the first version of the reader according to the NeXus application definition [NXsts](https://github.com/FAIRmat-NFDI/nexus_definitions/blob/fairmat/contributed_definitions/NXsts.nxdl.xml) which is a generic template of concepts' definition for STS and STM experiments. Later on, both application definitions and readers specific to the STM, STS and AFM will be available. To stay upto date keep visiting this page time to time. From now onwards we will mention STS referring both STM and STS.*** - -Main goal of STS Reader is to transform different file formats from diverse STS lab into STS community standard [STS application definition](https://github.com/FAIRmat-NFDI/nexus_definitions/blob/fairmat/contributed_definitions/NXsts.nxdl.xml), community defined template that define indivisual concept associated with STS experiment constructed by SPM community. -## STS Example -It has diverse examples from several versions (Generic 5e and Generic 4.5) of Nanonis software for STS experiments at [https://gitlab.mpcdf.mpg.de](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/tree/develop/docker/sts). But, to utilize that examples one must have an account at https://gitlab.mpcdf.mpg.de. If still you want to try the examples from the sts reader out, please reach out to [Rubel Mozumder](mozumder@physik.hu-berlin.de) or the docker container (discussed below). - -To get a detailed overview of the sts reader implementation visit [pynxtools-stm](https://github.com/FAIRmat-NFDI/pynxtools-stm). - -## STS deocker image -STS docker image contains all prerequisite tools (e.g. jupyter-notebook) and library to run STS reader. To use the image user needs to [install docker engine](https://docs.docker.com/engine/install/). - -STS Image: `gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter:latest` - -To run the STS image as a docker container copy the code below in a file `docker-compose.yaml` - -```docker -# docker-compose.yaml - -version: "3.9" - -services: - sts: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter:latest - ports: - - 8888:8888 - volumes: - - ./example:/home/jovyan/work_dir - working_dir: /home/jovyan/work_dir -``` - -and launch the file from the same directory with `docker compose up` command. From 557f6df78b4b07c9d1dfdc3fcba34905083e939c Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Thu, 10 Oct 2024 14:16:12 +0200 Subject: [PATCH 3/3] update links in examples README --- examples/README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/examples/README.md b/examples/README.md index 6ff784932..a8269f2c9 100644 --- a/examples/README.md +++ b/examples/README.md @@ -3,8 +3,7 @@ Here, we provide examples of how you can convert your data (raw data, numerical from your acquisition software or electronic lab notebook (ELN), into a NeXus/HDF5 file using the [built-in readers of pynxtools](https://fairmat-nfdi.github.io/pynxtools/reference/built-in-readers.html). -There is also [documentation](https://fairmat-nfdi.github.io/pynxtools/learn/dataconverter-and-readers.html) of the [dataconverter](../pynxtools/dataconverter) available. You can write a [reader](../pynxtools/dataconverter/readers) for your experimental technique -if it is not supported yet, see documentation [here](https://fairmat-nfdi.github.io/pynxtools/how-tos/build-a-plugin.html). +There is also [documentation](https://fairmat-nfdi.github.io/pynxtools/learn/dataconverter-and-readers.html) of the [dataconverter](../src/pynxtools/dataconverter/README.md) available. You can write a reader plugin if the data for your experimental technique is not supported yet, see documentation [here](https://fairmat-nfdi.github.io/pynxtools/how-tos/build-a-plugin.html). Note that `pynxtools` offers a number of FAIRmat-supported parsers/readers/data extractors for various experimental techniques via technique specific plugins. You can find the list [here](https://fairmat-nfdi.github.io/pynxtools/reference/plugins.html). You can find