User guide updates bpm panel

docs/css/custom_colors.css

@@ -10,6 +10,14 @@
   --color-cernpurple: #6e2466;
 }
 
+
+/* Useful to set a `cern` blue as primary in mkdocs.yml (dark mode) */
+[data-md-color-primary="cern"] {
+  --md-primary-fg-color: #0033a0;
+  --md-primary-fg-color--light: #9BAEDB;
+  --md-primary-fg-color--dark:  #0033A0;
+}
+
 /* General emphasis class */
 .omc-emph {
   color: var(--md-primary-fg-color);

docs/css/extra.css

@@ -90,12 +90,7 @@ a.cern_internal {
 
 }
 
-/* Useful to set a `cern` blue as primary in mkdocs.yml (dark mode) */
-[data-md-color-primary="cern"] {
-  --md-primary-fg-color: #0033a0;
-  --md-primary-fg-color--light: #9BAEDB;
-  --md-primary-fg-color--dark:  #0033A0;
-}
+
 
 /* Fix the Mathjax scrolling boxes issue */
 .md-typeset div.arithmatex {

docs/guis/betabeat/common_components.md

@@ -11,8 +11,15 @@ Independent of which tab is selected, some general components of the UI are comm
 
 All plots are running with the same back-end classes, which allows additional control via mouse and keyboard.
 
-Zooming can be achieved by drawing a rectangle with the left mouse button or with the shortcuts listed below.
-They also support the "hover" feature, which allows you to inspect additional details about the plotted points by hovering your mouse cursor over them.
+<figure>
+  <center>
+  <img src="../../assets/images/betabeat_gui/plot_with_hover.png" width="100%" alt="Beta-Beating Plot with BPM hover info." />
+  <figcaption>Hover info on a Beta-Beating Plot.</figcaption>
+  </center>
+</figure>
+
+- **Zoom**: Zooming can be achieved by drawing a rectangle with the left mouse button or with the shortcuts listed below.
+- **Hover Info**: The plots support the "hover" feature, which allows you to inspect additional details about the plotted points by hovering your mouse cursor over them.
 
 ### Shortcuts
 
@@ -124,5 +131,34 @@ As long as any task is running, there will also be a small animation on the righ
     but the actual task will keep running in the background.
     This needs to be implemented in the future.
 
+## File Opening Dialogs
+
+To make navigating between different folders easier, especially considering the deeply nested paths of `afs` and `nfs`,
+some shortcuts have been implemented into the file opening dialogs, which become available for all relavant dialogs **after [the beam selection window](beam_selection.md)**.
+They can be found at the top right of the dialog, and hovering them will show their functionality:
+
+<figure>
+  <center>
+  <img src="../../assets/images/betabeat_gui/open_files_folders.png" width="30%" alt="Special links in the file opening dialogs." />
+  <figcaption>Special links in the file opening dialogs.</figcaption>
+  </center>
+</figure>
+
+- **First Path** (:fontawesome-solid-check::fontawesome-solid-x:):
+Return to the initial path you were in when the window opened.
+- **Input Path** (:fontawesome-solid-circle-info:):
+Go to the path set as [_Input Path_ in the beam selection window](beam_selection.md#input).
+- **Output Path** (:fontawesome-solid-eye:):
+Go to the path set as [_Output Path_ in the beam selection window](beam_selection.md#output).
+- **Root Path** (**<>**)
+Go to the root-path for the current GUI instance, i.e. the path in which the accelerator-folder (e.g. `LHCB1`) is located.
+This is usually the date-directory within the output folder, unless you have choosen that folder as the _Output Path_,
+in which case it will be the same as the _Output Path_ (see the [Continue Analysis Admonition in the Beam Selection Window](beam_selection.md#folder-structure)).
+- **Fill Dir** (:fontawesome-solid-arrow-right:) _(Only available for the LHC and only if the folder is mounted)_:
+Go to the fill-directory of [the choosen accelerator](beam_selection.md#beam).
+- **Accelerator Dir** (:fontawesome-solid-star:) _(Only available for LHC, SPS, PS and PSB, and only if the folder is mounted)_:
+Go to the default OMC analyis directory of [the choosen accelerator](beam_selection.md#beam),
+which is usually the same as [the _Output Dir_, if the default is used in the beam selection window](beam_selection.md#output).
+
 [omc3]: https://github.com/omc3
 [pylhc]: https://github.com/PyLHC

docs/guis/betabeat/settings.md

@@ -88,10 +88,10 @@ This is in contrast to the other settings tabs, which control the settings passe
 
 - **Run Per-File Tasks in Parallel**:
   If active, tasks that are started together but can run independently per file will be run in individual tasks in parallel,
-  e.g. the `harpy` analysis will be run in parallel for each turn-by-turn file, even if started with multiple files selected.
-  Also, when running multiple optics analysis, but clicking the `Run per file` button, the analysis will be run in parallel for each file.
-  Conversely, if `Also run optics analysis` is selected, the first step of the `harpy` analsysis will be run sequentially per file,
-  as coordination between multiple tasks is not implemented.
+  e.g. the `harpy` analysis will be run in parallel for each turn-by-turn file, even if started with multiple files selected at once.
+  When running `optics analysis`, with _combine analysis_ deactivated, the analysis will be run in parallel for each file.
+  Conversely, if the user opts to also run the `optics analysis` directly from the BPM-Panel with _combine analysis_ activated, the `harpy` analysis of the files will be run sequentially per file in python,
+  as multiprocessing is not implemented in python.
 
 ## Tunes Tab
 
@@ -156,7 +156,7 @@ The fields are non-editable when it does not make sense in the current settings
   </center>
 </figure>
 
-The Harpy tab contains the settings for the harmonic `harpy` analysis.
+The Harpy tab contains the settings for the [harmonic `harpy` analysis][harpy_analysis].
 
 - **Files**:
   This field is not editable and automatically set when selecting TbT files in the [BPM Panel](bpm_panel.md) and running the analysis.
@@ -244,7 +244,7 @@ The `python` default is `""`, i.e. no suffix.
   </center>
 </figure>
 
-Most of the cleaning, for which the settings can be changed here, are part of the harmonic analysis module `harpy` in `omc3`
+Most of the cleaning, for which the settings can be changed here, are part of the [harmonic analysis module `harpy` in `omc3`][harpy_analysis]
 and will be executed during the "Analyse Spectrum" phase.
 Some of this procedure is also described on the [BPM filtering page][bpm_filtering].
 
@@ -254,12 +254,12 @@ Some of this procedure is also described on the [BPM filtering page][bpm_filteri
     is done within the cleaning module (see below).
 
 ??? info "Why is cleaning part of the harmonic analysis?"
-    Cleaning is part of the harmonic analysis in `harpy` as the [frequency analysis is done on the v-matrix of the SVD][harpy_ipac]:
+    Cleaning is part of the harmonic analysis in `harpy` as the [frequency analysis is done on the v-matrix of the SVD][harpy_analysis]:
     SVD is used to reduce the noise in the BPM data by selecting only the most important modes and in the same step also to detect bad bpms.
     As this decomposition is a linear transformation, the frequency analysis can be run directly on decomposed v-matrix, without
     having to re-compose the data into the time-domain, saving time and memory.
     The disadvantage is that, as we do not save the SVD matrices, there is no way to only run _cleaning_ without frequency analysis at the moment.
-    For more details, see [doi:10.18429/JACoW-IPAC2022-WEPOMS035][harpy_ipac].
+    For more details, see [this documentation][harpy_analysis] and [doi:10.18429/JACoW-IPAC2022-WEPOMS035][harpy_ipac].
 
 - **Active**:
   If active, the cleaning module is run during the "Analyse Spectrum" phase.
@@ -487,7 +487,6 @@ which is the `python`-internal representation of the accelerator and its setting
 
 [python-docs]: https://pylhc.github.io/omc3/
 [multiturn]: ../multiturn/gui.md
-[harpy_ipac]: https://accelconf.web.cern.ch/ipac2022/papers/wepoms035.pdf
 [bpm_filtering]: ../../measurements/physics/bpm_filtering.md
 [bad_bpms]: ../../measurements/physics/bpm_filtering.md#manual
 [isolation_forest_cleaning]: ../../measurements/physics/bpm_filtering.md#isolation-forest
@@ -496,4 +495,6 @@ which is the `python`-internal representation of the accelerator and its setting
 [gitlab_issue279]: https://gitlab.cern.ch/acc-co/lhc/lhc-app-beta-beating/-/issues/279
 [n_bpm_method]: https://journals.aps.org/prab/abstract/10.1103/PhysRevAccelBeams.20.111002
 [three_bpm_method]: https://repository.cern/records/eny2v-4y338
-[isolation_forest_issue]: https://github.com/pylhc/omc3/issues/184
+[isolation_forest_issue]: https://github.com/pylhc/omc3/issues/184
+[harpy_ipac]: https://accelconf.web.cern.ch/ipac2022/papers/wepoms035.pdf
+[harpy_analysis]: ../../measurements/physics/harpy.md

docs/measurements/physics/harpy.md

@@ -0,0 +1,20 @@
+# Harmonic Analysis with Harpy
+
+This page describes how the harmonic analysis is performed with the `harpy` module.
+If you want to know how to use the `harpy` module, refer to the [`omc3` analysis workflow][omc3_analysis].
+
+!!! todo "Implement this page"
+    Explain how harpy works.
+    Similar to [Malina - Harpy: A Fast, Simple and Accurate Harmonic Analysis with Error Propagation](https://accelconf.web.cern.ch/ipac2022/doi/JACoW-IPAC2022-WEPOMS035.html)
+    but more detail:
+
+    - SVD, Noise cleaning, Noise estimation
+    - Why numpy FFT? What about SUSSIX, LASKAR?
+    - Zero padding
+    - Binning
+    - Error propagation
+    - BPM cleaning
+    - Line identification
+
+
+[omc3_analysis]: ../../packages/omc3/analysis.md

mkdocs.yml

@@ -208,6 +208,7 @@ nav:
       - Error Propagation: measurements/physics/error_propagation.md
       - BPM-Calibration: measurements/physics/bpm_calibration.md
       - BPM-Filtering: measurements/physics/bpm_filtering.md
+      - Harmonic Analysis: measurements/physics/harpy.md
       - Coupling: measurements/physics/coupling.md
       - K-Mod: measurements/physics/kmod.md
       - Linear IR Optics: measurements/physics/ir_linear_optics.md