User Guide Updates: BBGui - Analysis Panel

docs/guis/betabeat/bpm_panel.md

@@ -16,7 +16,7 @@ and select the data to be analyzed further.
 
 !!! warning "Not yet implemented"
     The GUI does [not yet support loading of measurement groups][issue282]{target=_blank .cern_login} (i.e. kick groups).
-    The idea is to load all data from a single [kick-group, as defined in the Multiturn GUI](../multiturn/excitation.html#kick-groups) at once
+    The idea is to load all data from a single [kick-group, as defined in the Multiturn GUI][kick_groups] at once
     or monitor a currently active kick-group and load the files as they are created.
 
 ### Open Files
@@ -42,7 +42,7 @@ Use the ++"Open Files"++{.green-gui-button} button to open turn-by-turn data.
 Multiple files can be opened at once and are added to the current `Measurements` directory, as well as to the table of loaded files in the panel.
 If the file contained multiple bunches, they are added as separate entries (see [below](#table-of-loaded-files)).
 
-If the ["Analyse TbT files on opening" setting](settings.md#gui-tab) is active, a window will open to prompt the user with the ["Do analysis Dialog"][do_analysis_dialog].
+If the ["Analyse TbT files on opening" setting](settings.md#gui-tab) is active, a window will open to prompt the user with the ["Do analysis Dialog"](#do-analysis-dialog).
 
 !!! tip "Reopening Files"
     - If you are opening a file with the same filename as an already opened file, an error will be thrown.
@@ -130,6 +130,13 @@ You can select multiple measurements at once to compare them, but only one BPM p
     </center>
     </figure>
 
+!!! tip "Find BPMs"
+    The BPMs in the list are sorted by longitudinal position in model loaded when the file was opened.
+    Use the text field and the ++"Find BPM"++ button to quickly find BPMs in the list and **automatically select them**.
+    The text input is based on regular expressions and **the first BPM matching the pattern** will be selected.
+    Note that `^.*` and `.*$` will be added automatically to start and end of the string respectively,
+    to look for your pattern **anywhere** in the BPM name.
+
 ### Bad BPMs
 
 After [harmonic-analysis](#start-analysis) has been performed, the [bad BPMs][bpm_filtering] will be marked in red in the lists.
@@ -226,11 +233,12 @@ The _Suffix_-field will be automatically set from your suffix-choices in the [_H
 [issue283]: https://gitlab.cern.ch/acc-co/lhc/lhc-app-beta-beating/-/issues/283
 [issue285]: https://gitlab.cern.ch/acc-co/lhc/lhc-app-beta-beating/-/issues/285
 [bpm_filtering]: ../../measurements/physics/bpm_filtering.md
-[do_analysis_dialog]: analysis_panel.md#do-analysis-dialog
 [harpy_analysis]: ../../measurements/physics/harpy.md
+[kick_groups]: ../multiturn/excitation.md#kick-groups
 
 *[LHC]: Large Hadron Collider
 *[SPS]: Super Proton Synchrotron
 *[PS]:  Proton Synchrotron
 *[PSB]: Proton Synchrotron Booster
 *[BPM]: Beam Position Monitor
+*[BPMs]: Beam Position Monitors

docs/guis/betabeat/correction_panel.md

@@ -4,7 +4,9 @@ The `Correction` panel displays the corrections computed from the `Optics` panel
 
 It provides an `Open Knob Panel` button to access the LHC beam process list.
 
-## The Knob Panel
+## Knob Creation
+
+### The Knob Panel
 
 Through the `Knob Panel`, corrections can be provided directly inside the LHC beam system.
 
@@ -31,3 +33,5 @@ By selecting one, the user can examine or visualize the values attributed to eac
 
 !!! todo
     Include a screenshot of the Knob Panel view knobs chart
+
+## Correction Checks

docs/guis/betabeat/settings.md

@@ -12,7 +12,7 @@ The settings window can be initialized by the gear icon <span class="settings-ic
 
 !!! info "Defaults"
     The "Default" values given here are the defaults used in `python`,
-    These might not be up-to-date, check the [omc3 python documentation][python-docs]{:target="_blank"} for more information.
+    These might not be up-to-date, check the [omc3 python documentation][python-docs]{target=_blank} for more information.
     They might also be different from the defaults used in the GUI, as there are some defaults set upon startup determined by the selected machine.
     These GUI defaults are directly visible in the settings, while the `python` defaults are used when no value is given.
 
@@ -22,7 +22,7 @@ There is some general behaviour, that is true for all settings-tabs:
 
 - **Empty** text-fields are treated as _"Not given"_ and the **`python` defaults** will be used.
 - **Hovering the mouse over the label** of a setting will give additional information.
-  This is often the `help` provided by the corresponding `python` argument. Check the [omc3 python documentation][python-docs]{:target="_blank"} for more information.
+  This is often the `help` provided by the corresponding `python` argument. Check the [omc3 python documentation][python-docs]{target=_blank} for more information.
 - Entries in the settings that are lists (e.g. _Turns_, which will be `STARTTURN ENDTURN`) are given as **space-separated** values, NOT comma separated.
 - Of the buttons at the bottom, the top row refers to the current tab, the bottom row to all tabs.
 - Settings that have been changed since the last ++"Apply"++ / ++"Apply All"++ are <span style="color: red">highlighted in red</span> and can be reverted with the ++"Reset"++ button.
@@ -70,7 +70,7 @@ This is in contrast to the other settings tabs, which control the settings passe
 
 - **Analyse TbT Files on Opening**:
   If active and you open a turn-by-turn file, via the ++"Open Files"++{.green-gui-button} in the [BPM Panel](bpm_panel.md),
-  `harpy` analysis will be automatically started (for now: the user will be prompted with the ["Do analysis Dialog"](bpm_panel.md#do-analysis) directly after TbT import).
+  `harpy` analysis will be automatically started (for now: the user will be prompted with the ["Do analysis Dialog"](bpm_panel.md#do-analysis-dialog) directly after TbT import).
 
 - **Python Path**:
   Change the location of the `python` executable to be used to run the python scripts.
@@ -345,12 +345,12 @@ introduced by the AC-Dipole and if they are not found in the data, the optics an
   Files to to use for the optics analysis.
   These are the output files from `harpy`.
   This field is not editable and is only shown here, as `files` is an argument to `optics_measurement` and an attribute on the internal `OpticsSettings` class.
-  The actual files to use are chosen from the [Analysis Panel](analysis_panel.md), after which this field is automatically filled in when shown in the [Run Optics](analysis_panel.md#run-optics) popup window.
+  The actual files to use are chosen from the [Analysis Panel](analysis_panel.md), after which this field is automatically filled in when shown in the [Run Optics](analysis_panel.md#do-optics-dialog) popup window.
 
 - **Outputdir**:
   Directory to place to output of the optics analysis.
   The field is not editable and is only shown here, as `outputdir` is an argument to `optics_measurement` and an attribute on the internal `OpticsSettings` class.
-  The actual directory is chosen by the user per analysis, when setting an analysis name in the [Run Optics](analysis_panel.md#run-optics) popup window.
+  The actual directory is chosen by the user per analysis, when setting an analysis name in the [Run Optics](analysis_panel.md#do-optics-dialog) popup window.
 
 - **Calibrationdir**:
   Path to the directory containing the [calibration][bpm_calibration] files, used to rescale the BPM amplitudes and amplitude errors.

docs/guis/usage/guidelines.md

@@ -11,9 +11,9 @@ This is for three reasons:
 
 ### Model-View-Controller Architecture
 
-While not strictly enforced, our GUIs follow the [Model-View-Controller][mvc_wiki]{target="_blank"} architecture,
+While not strictly enforced, our GUIs follow the [Model-View-Controller][mvc_wiki]{target=_blank} architecture,
 as it is a very useful and therefore also very common GUI pattern.
-[A better explanation can be found here][mvc_geeks]{target="_blank"}, but this section summarizes a few key points relevant to our usecase.
+[A better explanation can be found here][mvc_geeks]{target=_blank}, but this section summarizes a few key points relevant to our usecase.
 
 The main philosophy of the MVC architecture is to separate the actual GUI elments, the _View_, from the underlying data, stored in the _Model_,
 and let the _Controller_ handle the communication between the two and with the user.
@@ -35,7 +35,7 @@ this code has been used for many years and probably will be continued to be used
 
 **Try to keep it clean!**
 
-Because GUI testing is hard and because we have easy access to old versions via [CAS][cas_cern]{target="_blank" .cern_internal},
+Because GUI testing is hard and because we have easy access to old versions via [CAS][cas_cern]{target=_blank .cern_internal},
 there is no tests suite and no review process for the `java` development and changes can be simply pushed to the `master` branch.
 
 Some "best practices" have been established through the years:
@@ -51,9 +51,9 @@ Some "best practices" have been established through the years:
 - Do not use `Strings` for file paths, for now we mostly use `File` objects (but see also the [Issue #239][issue_239]).
 
 !!! tip "Factory Pattern"
-    One pattern that you will find in different places of `java` code is the [factory design-pattern][factory_pattern_wiki]{target="_blank"}.
+    One pattern that you will find in different places of `java` code is the [factory design-pattern][factory_pattern_wiki]{target=_blank}.
     While useful in some scenarios, I personally (jdilly) find it too verbose and annoying to implement,
-    in the past there were even [scripts to automatically write the factory-code][internal_program_writer]{target="_blank"} because it needs so many lines of repeating code.
+    in the past there were even [scripts to automatically write the factory-code][internal_program_writer]{target=_blank} because it needs so many lines of repeating code.
 
     In particular, this pattern was used for the [creation of the `ExternalProgram` classes][factory_pattern_doc] to allow the setting of
     multiple attributes before even creating the class, without having to write multiple constructors

docs/measurements/physics/optics.md

@@ -0,0 +1,35 @@
+
+# Optics Analysis
+
+This page summarizes how the optics analysis is performed with the `measure_optics` module, from the physics point of view.
+If you want to know how to **use** the `measure_optics` module through `hole_in_one`, refer to the [`omc3` analysis workflow][omc3_analysis].
+
+!!! todo "Implement this page"
+    Explain how the analysis works.
+    If too long, maybe make sections their own page?
+
+## Linear Optics
+
+### Phase, Phase Advance and Special Phases
+
+### Beta from Phase
+
+### Beta from Amplitude
+
+### Action
+
+### Dispersion and Normalized Dispersion
+
+### Coupling
+
+See [Coupling](coupling.md)
+
+## Nonlinear Optics
+
+### Resonance Driving Terms
+
+### Combined Resonance Driving Terms
+
+### Chromatic Beating
+
+[omc3_analysis]: ../../packages/omc3/analysis.md

mkdocs.yml

@@ -209,6 +209,7 @@ nav:
       - BPM-Calibration: measurements/physics/bpm_calibration.md
       - BPM-Filtering: measurements/physics/bpm_filtering.md
       - Harmonic Analysis: measurements/physics/harpy.md
+      - Optics Analysis: measurements/physics/optics.md
       - Coupling: measurements/physics/coupling.md
       - K-Mod: measurements/physics/kmod.md
       - Linear IR Optics: measurements/physics/ir_linear_optics.md