From 46347ec467448745de64c2d9dddb49db6caac9f2 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Tue, 12 Mar 2024 14:46:07 +0100 Subject: [PATCH 1/2] fix nexus conversion tutorial and its links --- docs/tutorial/converting-data-to-nexus.md | 24 ++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/docs/tutorial/converting-data-to-nexus.md b/docs/tutorial/converting-data-to-nexus.md index 08104bac2..8bc158987 100644 --- a/docs/tutorial/converting-data-to-nexus.md +++ b/docs/tutorial/converting-data-to-nexus.md @@ -21,20 +21,20 @@ You will have ## Setup -We use a Python tool to make converting our research data easier. This has a number of [readers](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers) that support multiple file formats. You can browse the separate folders to find the reader that might work for you. A generic reader is the [JSON Map Reader](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers/json_map). +We use a Python tool to make converting our research data easier. This has a number of [readers](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers) that support multiple file formats. You can browse the separate folders to find the reader that might work for you. A generic reader is the [JSON Map Reader](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers/json_map). In addition, we provide multiple [reader plugins](https://github.com/FAIRmat-NFDI/pynxtools/tree/master?tab=readme-ov-file#plugins) for different experimental techniques. -We will use the [XPS Reader](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers/xps) with a [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) file (.sle) as an example. +We will use the [XPS reader plugin](https://github.com/FAIRmat-NFDI/pynxtools-xps) with a [SpecsLabProdigy](https://www.specs-group.com/nc/specs/products/detail/prodigy/) file (file extension: .sle) as an example. #### Steps -1. Download the example files from here: [Example files](https://download-directory.github.io/?url=https://github.com/FAIRmat-NFDI/pynxtools/tree/master/examples/xps) +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) 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 ``` -3. Install [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools/tree/master?tab=readme-ov-file#installation) +3. Install [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools/tree/master?tab=readme-ov-file#installation) with the [XPS reader plugin](https://github.com/FAIRmat-NFDI/pynxtools-xps): ```console -pip install git+https://github.com/FAIRmat-NFDI/pynxtools.git +pip install pynxtools[xps] ``` 4. Verify you can run the ```dataconverter``` in a terminal window. Open a terminal with the Python environment where you installed ```pynxtools```. Then type the following: ```console @@ -43,21 +43,23 @@ dataconverter --help ## Converting the example files -Once you have your files copied into the working directory. Your directory structure should look like this: +Once you have your files copied into the working directory, your directory structure should look like this: ``` ├── README.md ├── EX439_S718_Au.sle -├── params.yaml -└── eln_data_sle.yaml +├── eln_data_sle.yaml +└── params.yaml ``` +The ```eln_data_sle.yaml``` YAML file is another data file containing additional information (e.g., information about the experimentator) that is not provided in the main data file. + Next, you will run the conversion routine from your Python environment: ```console dataconverter --params-file params.yaml ``` -Here we use a params.yaml parameter file to configure the converter. You can try out [other examples from pynxtools](https://github.com/FAIRmat-NFDI/pynxtools/tree/documentation/examples) - -This will create a file called ```Au_25_mbar_O2_no_align.nxs``` in your current directory. +Here we use a ```params.yaml``` parameter file to configure the converter. This will create a file called ```Au_25_mbar_O2_no_align.nxs``` in your current directory. **Congrats! You now have a FAIR NeXus file!** + +You can try out [other examples from pynxtools](https://github.com/FAIRmat-NFDI/pynxtools/tree/documentation/examples). From 4176b2a4ed4748c371e02dca6360e398077d7c8f Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Tue, 12 Mar 2024 15:09:07 +0100 Subject: [PATCH 2/2] fix link to other examples --- 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 8bc158987..cbe9c2813 100644 --- a/docs/tutorial/converting-data-to-nexus.md +++ b/docs/tutorial/converting-data-to-nexus.md @@ -62,4 +62,4 @@ Here we use a ```params.yaml``` parameter file to configure the converter. This **Congrats! You now have a FAIR NeXus file!** -You can try out [other examples from pynxtools](https://github.com/FAIRmat-NFDI/pynxtools/tree/documentation/examples). +You can try out [other examples from pynxtools](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/examples).