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+(user.saxs.data_analysis)=
+# Data analysis
+
+We can access the online computing resources from the beamline consoles when logged in as the e-account.
+
+## Allocation of nodes
+
+Check available nodes and allocate one:
+
+```bash
+sinfo
+salloc -A csaxs -p csaxs -w [ra-c-110]
+ssh -Y [ra-c-110]
+```
+
+Or for a GPU node:
+
+```bash
+salloc -A csaxs -p gpu-csaxs --gpus=4 [-w ra-gpu-003]
+ssh -Y [ra-gpu-003]
+```
+
+(note that we need to ask them to explicitly use one of our GPU nodes there, and this needs a couple of days to set up)
+
+**The home directory is the p group.** To go to the raw directory we need to navigate there:
+
+```bash
+cd /sls/x12sa/data/[p22598]/raw
+```
+
+## Python tools
+
+### Python package installation
+
+Anaconda is no longer supported. Packages should now be installed directly using `pip`.
+
+For example, `pyFAI` can be installed as follows:
+
+```bash
+module load Python/3.11.11
+pip install "pyFAI[gui]"
+```
+
+To launch the `pyFAI` applications:
+
+```bash
+# Detector calibration
+python -m pyFAI.app.calib2
+
+# Batch integration
+python -m pyFAI.app.integrate
+```
+
+### Recommended: using a Python virtual environment
+
+For long-term maintainability and reproducibility, it is recommended to use a dedicated Python virtual environment.
+
+#### Create a virtual environment
+
+```bash
+cd /sls/x12sa/data/[p-group]/raw
+
+module load Python/3.11.11
+mkdir python-env
+cd python-env
+
+# Create a virtual environment named ".venv"
+python3 -m venv .venv
+
+# Activate the environment
+source .venv/bin/activate
+
+# Install required packages
+pip install "pyFAI[gui]"
+```
+
+#### Use an existing virtual environment
+
+```bash
+cd /sls/x12sa/data/[p-group]/raw/python-env
+source .venv/bin/activate
+```
+
+### Troubleshooting
+
+If you encounter the following error when launching GUI applications (e.g. `pyFAI-calib2`):
+
+```text
+X11 connection rejected
+```
+
+reconnect to the analysis node with X11 forwarding enabled:
+
+```bash
+ssh -X [ra-c-110]
+```
+
+and then reactivate the virtual environment before launching the application.
+
+## Use Jupyter Notebook / Lab
+
+Create a virtual environment following the instructions above, then:
+
+```bash
+pip install jupyter
+```
+
+To run Jupyter Lab:
+
+```bash
+jupyter lab --port 6006 --ip $(hostname) --no-browser
+```
+
+## Setup online radial integration on Jungfraujoch
+
+1. **Calibrate the detector using pyFAI.**
+
+ Analyze a calibration scan carefully with `pyFAI` and save the resulting **PONI** file and **pixel mask**. Also determine the beam center position.
+
+ :::{note}
+ As of 2026-06-18, Jungfraujoch only accepts `uint32` TIFF mask files. If the mask generated by `pyFAI` is stored as `uint8`, it needs to be converted to the required format before uploading.
+ To do this (from the home directory `/sls/x12sa/data/[p-group]/raw/`):
+
+ - Activate the python environment: `source mask/.mask/bin/activate`
+ - Run `python convert_mask_format.py -i -o