moved ideas to codi, omc3 all around

Author: JoschD

docs/guis/about.md

@@ -11,18 +11,18 @@ Of these, only the Beta-Beat GUI is currently developed by the team.
 ## Running the GUIs
 
 The GUIs can be started from your development environment or via deployed `.jnlp` from the archives:
-
-=== "Beta-Beat"
-
-    - Latest [Beta-Beating production version][prod_bbgui]{target=_blank}.
-    - Latest [Beta-Beating development version][dev_bbgui]{target=_blank}.
-    - Complete [list of releases][releases_bbgui]{target=_blank}.
 
 === "Beta-Beat-OMC3"
 
     - Latest [Beta-Beating production version][prod_bbgui_omc3]{target=_blank}.
     - Latest [Beta-Beating development version][dev_bbgui_omc3]{target=_blank}.
     - Complete [list of releases][releases_bbgui_omc3]{target=_blank}.
+
+=== "Beta-Beat (Legacy)"
+
+    - Latest [Beta-Beating production version][prod_bbgui]{target=_blank}.
+    - Latest [Beta-Beating development version][dev_bbgui]{target=_blank}.
+    - Complete [list of releases][releases_bbgui]{target=_blank}.
 
 === "Kmod"
 
@@ -66,6 +66,26 @@ The following are required to run the GUIs:
 
 You may encounter the following errors:
 
+#### Running in the CCC in 2025
+
+On the CCC terminals, there are some issues related to finding the correct java path,
+which affects `NXCals` extraction.
+
+To avoid this, close all windows and CCMs and then run:
+
+```bash
+/user/slops/data/LHC_DATA/OP_DATA/Betabeat/launch_ccm.sh
+```
+
+This script performs the follwowing commands, which could also be done manually in a terminal:
+
+- Create a kerberos ticket: `kinit lhcop`
+- Adapt the path/set `JAVA_HOME` to use the correct java: `export PATH=/bin:$PATH`  and/or `export JAVA_HOME=/usr/java/jdk`  (either should be fine)
+- run `ccm` or `/mcr/bin/ccm`
+
+Then select `LHCOP` and launch the Beta-Beat GUI from the new CCM window.
+
+
 #### Problems with execution due to disabled Java
 
 If you encounter a complaint about `Java` being too old, try using `/mcr/bin/jws`.

docs/guis/betabeat/ampdet.md

@@ -0,0 +1 @@
+# Amplitude Detuning Analysis

docs/guis/betabeat/analysis_panel.md

@@ -38,7 +38,7 @@ After cleaning is finished, the optics function can be computed from the harmoni
   </center>
 </figure>
 
-### Additional cleaning based on the tune ##
+### Additional cleaning based on the tune
 Additionally, BPMs can be cleaned based on the tune values computed by harmonic analysis. The chart displaying the selected columns of harmonic analysis data has interactive cursors. These cursors can be moved manually to set the thresholds for tune-based cleaning - all BPMs having tune values outside of the set range will be removed. The cursors can be also automatically set to e.g. 4 sigmas deviation from the average tune values over all BPMs.
 
 ### Summary of cleaning steps before optics analysis
@@ -54,6 +54,12 @@ The `Frequency` tab displays the computed frequencies for every BPM.
 A `Get Optics` button can be used to start the optics calculation.
 This will call an external python script again, with the results available in the [Optics Panel](optics_panel.md).
 
+### Nattune Updater
+
+* You can set a frequency range and it does not redo the analysis but just picks the highest peak in that range and assigns it to `NATTUNE` in the lin-file.
+* This should be very helpful for amplitude detuning analysis.
+* Do NOT use the Nattune-Updater if you have free kicks (it adds a `NATTUNE`-Column to the lin-file).
+
 !!! todo
     Include a screenshot of the frequency panel.
 

docs/guis/betabeat/beam_selection.md

@@ -1,43 +1,23 @@
 # The beam selection Window
 
+!!! tip "Setting Your Defaults"
+    You can set all entries in this window to your preferred defaults for a quick start!
+    Check the [Defaults Page](defaults.md) for more details.
+
 !!! todo
     Include screenshot of Beam-Selection Window and describe the settings.
 
+### Python
 
-!!! tip "Setting Your Defaults"
-    The GUI defaults to specific locations for which `Beta-Beat.src` directory to use, the input path of you data, etc.
-    Different key-value pairs can be set inside for the desired defaults, for example:
-    
-    ```bash
-    beam = LHCB1_RUNII_2018
-    inputPath = /some/afs/location/with/your/data/
-    outputPath = /some/afs/location/with/your/results/
-    betaBeatPath = /some/afs/location/with/your/Beta-Beat.src/
-    loadData=True
-    ```
-    These values can be set by a file named `bbgui_user.properties` (with the above syntax) in either the current working directory, from where you run the GUI, or in your home folder. 
-    The latter is only used if there is no such file in the current working directory.
-
-    If you want to use a specific file located anywhere, you can also give the path to this file as the first and only argument when starting the GUI.
-    It is also possible to set each of these default values by passing them as flag arguments to the GUI call, e.g: 
-    
-    ```
-    --beam LHCB1_RUNII_2018 --inputPath /some/afs/location/with/your/data/
-    ```
-
-??? tip "Additional Default Settings"
-    Additionally, there are some settings that can only be set via arguments.
-    Their keys and default values are:
-    
-    ```bash
-    oldFolderStructure=True
-    consoleLogging=False
-    checkFreeSpace=False
-    ```
+In the Beam-Selection Window you need to give it a python-binary (e.g. `venv/bin/python`).
+Best would be if you have a local virtual environment.
+This **needs to have omc3 installed as a package**.
+See [omc3 on github][omc3_github_getting_started]{target=_blank}.
+```bash
+pip install git+https://github.com/pylhc/omc3.git
+```
+This is because python calls are now made by module, i.e.:
+```bash
+python -m omc3.module arg1 arg2 ...
+```
 
-    - `oldFolderStructure` refers to the folder structure, where the `models` folder is at top level and contains the machines as subdirectories.
-      Setting this value to `False` assumes (and creates) the models in a `Models` folder on the same level as `Measurements` and `Results`, i.e. within the machine-folders.
-    - `consoleLogging` activates additional logging into the terminal.
-      The effect is only visible if the GUI was started from the console.
-    - `checkFreeSpace` activates a quick check of the available space upon start of the GUI.
-      The result of this check is logged in the console, and hence also only visible if the GUI is started via terminal command.

docs/guis/betabeat/betabeatsource.md

@@ -0,0 +1,7 @@
+# BetaBeat.src
+
+Since 2025, the former `omc3` branch has been moved to the `master` branch of the GUI and is now the default for all new users.
+The "BetaBeat.src" branch of the GUI has been retired from `master` to the `BetaBeatSrc` branch
+and is no longer under active development.
+
+Legacy version are still available on CAS.

docs/guis/betabeat/defaults.md

@@ -0,0 +1,60 @@
+# Defaults
+
+## Beam Selection Defaults
+
+(For details see the [Beam Selection](beam_selection.md) page)
+
+The GUI defaults to specific locations for which `python` binary to use, the input path of you data, etc.
+Different key-value pairs can be set inside for the desired defaults, for example:
+
+```bash
+beam = LHCB1
+inputPath = /some/afs/location/with/your/data/
+outputPath = /some/afs/location/with/your/results/
+pythonPath = /some/afs/location/with/your/python-env/bin/python
+loadData=False  # True: Load already existing data in the outputPath into the GUI
+oldFolderStructure=False   # True: Put `models` folder at top level instead of the current machine folder (BBS legacy)
+```
+These values can be set by a file named `bbgui_user.properties` (with the above syntax) in either the **current working directory** (from where you run the GUI), or in **your home folder**. 
+The latter is only used if there is no such file in the current working directory.
+
+If you want to use a specific file located anywhere, you can also give the path to this file as the first and only argument when starting the GUI.
+It is also possible to set each of these default values by passing them as flag arguments to the GUI call, e.g: 
+
+```
+--beam LHCB1 --inputPath /some/afs/location/with/your/data/
+```
+
+## Additional GUI Defaults
+
+Additionally, there are some GUI settings that can either only be set via arguments or
+modify the default value in the GUI:
+
+```bash
+consoleLogging=True   # activate additional logging into the terminal (only visible if started from terminal)
+checkFreeSpace=True   # check fee space at GUI start (only visible if started from terminal)
+
+# BPM-Panel
+runOptics=True  # set the tickbox next to the `Analyse` button to also run the optics analysis by default
+
+# Analysis-Panel
+autoclean.limit=0.1  # set the autoclean limit 
+clean.sigmas=2  # set the number of sigmas for the autoclean
+clean.bounds=0.7  # when cleaning, this ratio needs to remain otherwise the cleaning is aborted
+
+# Amplitude-Detuning-Window 
+ampdet.tunecut=0.05  # limit around the given tune to exclude from the natural tune when fitting
+ampdet.window=100  # length of the moving average window for the natural tune
+ampdet.outlierLimit=0.0002   # Cut on outliears around the mean 
+ampdet.usePreviousBBQ=True  # Do not extract BBQ data if there is already data present
+```
+
+For more details about these functions see the [BPM-Panel](bpm_panel.md), [Analysis-Panel](analysis_panel.md) and [Amplitude-Detuning](ampdet.md) pages.
+
+## Default Settings
+
+(For details see the [Settings](settings.md) page)
+
+When saving the GUI settings, a similar file `settings_xxx.properties` is created.
+Instead of loading these settings manually, you can also copy all or a selection of these settings
+from the output file into the `bbgui_user.properties` and they will be set automatically when the GUI is started.

docs/guis/betabeat/gui.md

@@ -6,10 +6,8 @@ This section provides a short overview for the main features.
 
 !!! info
     The code documentation of the Beta-Beat GUI can be found on CERN's gitlab pages.
-    The master and OMC3 branches are generated:
-
+      
       * [Master branch][bbgui_doc_bbsrc]{target=_blank}
-      * [OMC3 branch][bbgui_doc_omc3]{target=_blank}
 
 
 The GUI provides several panels, each for a defined use and with a set of options and results:
@@ -22,7 +20,15 @@ The GUI provides several panels, each for a defined use and with a set of option
 This site will guide you through the GUI's layout and functionality.
 For starters, check out [the basics of running the GUI](../about.md).
 
+!!! warning "Bug Reporting"
+    If you find bugs, please create [issues][betabeat_gui_gitlab_issues]{target=_blank} with the `OMC3-GUI` label.
 
-[bbgui_doc_bbsrc]: https://lhc-app-beta-beating.docs.cern.ch/master/
-[bbgui_doc_omc3]: https://lhc-app-beta-beating.docs.cern.ch/omc3/
+## General Notes
+
+### Opening Files
 
+* Each tab has now an <span style="color:green;">Open Files</span> button, which opens only the files specific to this tab.
+* The magic <span style="color:green">**+**</span> button is gone, as its functionality was confusing (and there were different stories about its workings).
+
+[bbgui_doc_bbsrc]: https://lhc-app-beta-beating.docs.cern.ch/master/
+[betabeat_gui_gitlab_issues]: https://gitlab.cern.ch/acc-co/lhc/lhc-app-beta-beating/-/issues

docs/guis/betabeat/omc3.md

@@ -63,4 +63,11 @@ The following methods implement different correction algorithms:
 The results are outputted in the `changeparameters` files.
 These files store the magnet names and corresponding correction strengths.
 
-They are also displayed in the [Correction Panel](correction_panel.md).
+They are also displayed in the [Correction Panel](correction_panel.md).
+
+
+### Optics Plotting
+
+* RDT and CRDT plots are added dynamically depending on the files present in the respective folders.
+* Nicer names and more structure in the tree.
+* Backend was rewritten, so it is now more modular and easier to add new plot-types.

docs/guis/betabeat/optics_panel.md

@@ -0,0 +1,16 @@
+# Plotting
+
+All plots are running with the same backend classes, which allows additional control via mouse and keyboard.
+
+
+## Keyboard/Mouse Shortcuts
+
+* ++lbutton++ : Draw and zoom into rectangle.
+* ++mbutton++ : Auto-zoom (in 3 Steps: 4σ, 3σ, 2σ).
+* ++rbutton++ : Undo last step.
+* ++shift+rbutton++ : Undo all steps (reset plot).
+* ++mousewheel++ : Zoom relative to mouse position.
+* ++shift+mousewheel++ : Zoom y-axis relative to mouse position.
+* ++alt+mousewheel++ : Zoom relative to plot center.
+* ++shift+alt+mousewheel++ : Zoom y-axis relative to plot center.
+