6 changed files with 118 additions and 48 deletions
@@ -38,11 +38,11 @@ Every content page starts with a **cross-reference label** followed by a single
 top-level heading:

 ```md
-(user.saxs.data_analysis)=
-# Data analysis
+(user.saxs.online_integration)=
+# Setup online radial integration on Jungfraujoch
 ```

- The label `(user.saxs.data_analysis)=` is what other pages, the section landing
+- The label `(user.saxs.online_integration)=` is what other pages, the section landing
  pages, and the `{ref}` role link to. **Do not delete or rename it** without
  updating every reference, or links silently break.
 - The `# Title` is the page's H1. Sphinx needs exactly one; section pages do not
@@ -81,7 +81,7 @@ Available types include `note`, `tip`, `important`, `warning`, `caution`, `dange
 - **To another page in this documentation**, link by its label, not by file path:

  ```md
-  See {ref}`the data analysis guide <user.saxs.data_analysis>`.
+  See {ref}`the Jungfraujoch setup guide <user.saxs.online_integration>`.
  ```

 - **External links** use ordinary Markdown: `[pyFAI](https://pyfai.readthedocs.io)`.
@@ -114,7 +114,7 @@ Available types include `note`, `tip`, `important`, `warning`, `caution`, `dange
   hidden: true
   ---

-   data_analysis
+   online_integration
   <name>
   ```
   ````
@@ -1,5 +1,5 @@
-(user.saxs.data_analysis)=
-# Data analysis
+(user.data_analysis.computing)=
+# Online data analysis

 We can access the online computing resources from the beamline consoles when logged in as the e-account.

@@ -16,12 +16,23 @@ ssh -Y [ra-c-110]
 Or for a GPU node:

 ```bash
-salloc -A csaxs -p gpu-csaxs --gpus=4 [-w ra-gpu-003]
+salloc -A csaxs -p gpu-csaxs --gpus=4 [-w ra-gpu-003] --mem=100G -n 8
 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)

+### Specifications of the computing nodes
+
+A few examples of the available nodes:
+
+| Node | CPU | Cores | Memory | GPUs | Partition |
+|---|---|---|---|---|---|
+| `ra-c-110` | Intel Xeon 6152 | 44 | 377 GB | — | `csaxs` |
+| `ra-gpu-003` | AMD EPYC 7452 | 64 | 1007 GB | 4x NVIDIA A100 (40 GB) | `gpu-csaxs` |
+| `ra-gpu-007` | Intel Xeon 6530 | 64 | 1007 GB | 4x NVIDIA L40S (46 GB)| `gpu-csaxs` |
+
+
 **The home directory is the p group.** To go to the raw directory we need to navigate there:

 ```bash
@@ -81,7 +92,7 @@ cd /sls/x12sa/data/[p-group]/raw/python-env
 source .venv/bin/activate
 ```

-### Troubleshooting
+#### Troubleshooting

 If you encounter the following error when launching GUI applications (e.g. `pyFAI-calib2`):

@@ -97,7 +108,7 @@ ssh -X [ra-c-110]

 and then reactivate the virtual environment before launching the application.

-## Use Jupyter Notebook / Lab
+### Use Jupyter Notebook / Lab

 Create a virtual environment following the instructions above, then:

@@ -110,40 +121,15 @@ To run Jupyter Lab:
 ```bash
 jupyter lab --port 6006 --ip $(hostname) --no-browser
 ```
+## cSAXS matlab scripts

-## Setup online radial integration on Jungfraujoch
+To use the cSAXS matlab scripts we can go to the `cxs_software` package in the raw folder. 

-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).
-   :::
+In base we can do:
+```bash
+source setup-environment.sh 
+```
+And then we can use Matlab interactively as usual.
+```bash
+matlab &
+```
@@ -0,0 +1,34 @@
+(user.data_analysis)=
+# Data analysis
+Welcome to the data analysis section of the cSAXS beamline. 
+
+```{toctree}
+---
+maxdepth: 2
+hidden: true
+---
+
+computing
+
+```
+
+
+***
+
+````{grid} 2
+:gutter: 5
+
+```{grid-item-card}
+:link: user.data_analysis.computing
+:link-type: ref
+:img-top: /assets/index_user_guide.svg
+:text-align: center
+:class-item: index-card
+
+## Online data analysis
+
+Allocating compute nodes, programming using Python and Matlab during the beamtime.
+```
+
+````
+For offline analysis, more detailed documentation on use of slurm on Ra, description of NoMachine setup is available at https://dari.pages.psi.ch/ra/compute.html/.
@@ -0,0 +1,37 @@
+(user.saxs.online_integration)=
+# 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).
+   :::
@@ -8,7 +8,7 @@ maxdepth: 2
 hidden: true
 ---

-data_analysis
+online_integration

 ```

@@ -19,7 +19,7 @@ data_analysis
 :gutter: 5

 ```{grid-item-card}
-:link: user.saxs.data_analysis
+:link: user.saxs.online_integration
 :link-type: ref
 :img-top: /assets/biotech.svg
 :text-align: center
@@ -27,7 +27,7 @@ data_analysis

 ## Data analysis

-Allocating compute nodes, pyFAI installation and usage, and online radial integration on Jungfraujoch.
+Setup of online radial integration on Jungfraujoch.
 ```

 ````
@@ -11,6 +11,7 @@ hidden: true
 before_you_arrive/before_you_arrive.md
 ptychography/ptychography.md
 saxs/saxs.md
+data_analysis/data_analysis.md

 ```

@@ -55,5 +56,17 @@ All about ptychography measurements and reconstructions.

 All about SAXS measurements and analysis.
 ```
+```{grid-item-card}
+:link: user.data_analysis
+:link-type: ref
+:img-top: /assets/biotech.svg
+:text-align: center
+:class-item: index-card
+
+## Data analysis
+
+All about data analysis during the beamtime.
+```
+

 ````