docs/user/saxs/data_analysis.md

@@ -0,0 +1,149 @@
+(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 <input .tif file path> -o <output .tiff file path>`
+   :::
+
+2. **Update the BEC configuration.**
+
+   Update the detector distance and beam center coordinates in the BEC configuration files using the calibration results.
+
+3. **Configure Jungfraujoch.**
+
+   Open the **Jungfraujoch Expert Configuration** panel in the frontend interface, for example:
+
+   ```text
+   http://sls-jfjoch-001:8080/frontend
+   ```
+
+   - Upload the pixel mask under **Pixel Mask**.
+   - Fill in the required parameters under **Azimuthal Integration Settings**.
+   - Make sure to enable **Force CPU calculation in FPGA workflow**.
+   - After uploading a new configuration, do not press "initialize", as this will remove all the previously uploaded configuration.
+
+4. **Detector rotation (if required).**
+
+   :::{note}
+   Adding rotation of the detector still needs to be documented (likely configured in the BEC configuration).
+   :::

docs/user/saxs/saxs.md

@@ -1,5 +1,39 @@
 (user.saxs)=
-# Saxs
+# SAXS
+Welcome to the SAXS section of the cSAXS beamline.
+
+```{toctree}
+---
+maxdepth: 2
+hidden: true
+---
+
+data_analysis
+
+```
 
 
-## Beamtime allocation
+***
+
+````{grid} 2
+:gutter: 5
+
+```{grid-item-card}
+:link: user.saxs.data_analysis
+:link-type: ref
+:img-top: /assets/biotech.svg
+:text-align: center
+:class-item: index-card
+
+## Data analysis
+
+Allocating compute nodes, pyFAI installation and usage, and online radial integration on Jungfraujoch.
+```
+
+````
+
+
+## Reference documents
+
+- {download}`SAXS standards plate (PDF) <SAXS_standards_plate.pdf>`
+