From 133cd2c2676b02deba749488e0f603a0e3fe0254 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Fri, 2 Feb 2024 10:31:54 +0100 Subject: [PATCH] update read_nexus readme --- pynxtools/nexus/README.md | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/pynxtools/nexus/README.md b/pynxtools/nexus/README.md index df04940dc..2700b62b6 100644 --- a/pynxtools/nexus/README.md +++ b/pynxtools/nexus/README.md @@ -1,3 +1,6 @@ +# Debugger and + + 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 NeXus base classes and application definitions to which the file refers to. @@ -23,6 +26,11 @@ read_nexus [Options] ``` +The following example dataset can be used to test the `read_nexus` 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). + +## Using a different set of NeXus definitions _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 definitions in its bundle._ @@ -33,12 +41,8 @@ An environmental variable can be set as follows: export 'NEXUS_DEF_PATH'= ``` -Following example dataset can be used to test `read_nexus` 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). - - -A note to Windows users: if you run `read_nexus` from `git bash`, you need to set the environmental variable +## A note to Windows users +If you run `read_nexus` from `git bash`, you need to set the environmental variable `MSYS_NO_PATHCONV` to avoid the [path translation in Windows Git MSys](https://stackoverflow.com/questions/7250130/how-to-stop-mingw-and-msys-from-mangling-path-names-given-at-the-command-line#34386471). The easiest way is to prefix the `read_nexus` call with `MSYS_NO_PATHCONV=1`: