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Update SLE examples and readme #12

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9 changes: 4 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,20 +14,20 @@ Learn how to manage [python versions](https://github.com/pyenv/pyenv) and
Install this package with

```shell
pip install git+https://github.com/FAIRmat-NFDI/pynxtools_xps.git
pip install git+https://github.com/FAIRmat-NFDI/pynxtools-xps.git
```

for the latest development version.


# Purpose
This pynxtools reader plugin is used to translate diverse file formats from the scientific community and technology partners
This reader plugin for [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools) is used to translate diverse file formats from the scientific community and technology partners
within the field of X-ray photoelectron spectroscopy into a standardized representation using the
[NeXus](https://www.nexusformat.org/) application definition [NXmpes](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXmpes.html#nxmpes).

## Supported file formats
The reader decides which parser to use based on the file extension of the files provided. For the main XPS files, the following file extensions are supported:
- .sle: [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) files, propietary format of SPECS GmbH (v1.6)
- .sle: [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) files, propietary format of SPECS GmbH (1 and v4)
- .xml: SpecsLab 2files, XML format from SPECS GmbH (v1.6)
- .vms: VAMAS files, ISO standard data transfer format ([ISO 14976](https://www.iso.org/standard/24269.html)), both in regular and irregular format
- .xy: SpecsLabProdigy export format in XY format (including all export settings)
Expand All @@ -47,8 +47,7 @@ An example script to run the XPS reader in pynxtools:
--input-file $<eln-file path> \
--output <output-file path>.test.nxs
```
Note that none of the supported file format have data/values for all required and recommended fields and attributes in NXmpes. In order for the validation step of the **XPS** reader to pass,
you need to provide an ELN file that contains the missing values. An example can be found in [*pynxtools_xps/examples*](https://github.com/FAIRmat-NFDI/pynxtools-xps/tree/main/examples).
Note that none of the supported file format have data/values for all required and recommended fields and attributes in NXmpes. In order for the validation step of the XPS reader to pass, you need to provide an ELN file that contains the missing values. An example can be found in [*pynxtools_xps/examples*](https://github.com/FAIRmat-NFDI/pynxtools-xps/tree/main/examples).


# Contributing
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12 changes: 12 additions & 0 deletions examples/.sle/README.md
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@@ -0,0 +1,12 @@
# Example for .sle data

This is an example for the [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) .sle files, which is the propietary format of SPECS GmbH. The SpecsLabProdigy software version is v4.63.1. The example conversion can be run with the following command.

```console
user@box:~$ dataconverter --params-file params.yaml
```

Not that the `params.yaml` file contains the `remove_align` keyword which is special for the SLE parser. It allows removal of alignment spectra that were taken during the experiment. For this example, it considerably speeds up the conversion.

## Contact person in FAIRmat for this example
Lukas Pielsticker
21 changes: 8 additions & 13 deletions examples/README.md
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@@ -1,22 +1,17 @@
# XPS Reader
# Examples for the XPS

## What is this reader?
Here, you can find working examples of XPS-to-NeXus conversion using the latest [NXmpes](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXmpes.html#nxmpes) application definition and the latest development version of [pynxtools-xps](https://github.com/FAIRmat-NFDI/pynxtools-xps).

This reader supports converting X-ray photoelectron spectroscopy into a NeXus formatted file. The application definiton it follows is [NXmpes](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXmpes.html#nxmpes).
This reader supports converting X-ray photoelectron spectroscopy into a NeXus formatted file. You can find examples for the supported file formats in the individual subfolders.

## Supported file formats
The reader decides which parser to use based on the file extension of the files provided. For the main XPS files, the following file extensions are supported:
- .sle: [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) files, propietary format of SPECS GmbH (v1.6)
- .xml: SpecsLab 2files, XML format from SPECS GmbH (v1.6)
- .vms: VAMAS files, ISO standard data transfer format ([ISO 14976](https://www.iso.org/standard/24269.html)), both in regular and irregular format
## Existing examples
- .sle: [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) file, propietary format of SPECS GmbH (software version: v1.6)
- .xml: SpecsLab 2files, XML format from SPECS GmbH (software version: v4.63)
- .vms: VAMAS files, ISO standard data transfer format ([ISO 14976](https://www.iso.org/standard/24269.html)), in regular format
- .xy: SpecsLabProdigy export format in XY format (including all export settings)
- .txt:
- exported by [Scienta Omicron](https://scientaomicron.com/en) instruments
- exported by [CasaXPS](https://www.casaxps.com/) analysis software

```console
user@box:~$ dataconverter --params-file params.yaml
```

## Contact person in FAIRmat for this reader
## Contact person in FAIRmat for these example
Lukas Pielsticker
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