Merge branch 'master' into emaclean-patch-1

Author: fsoubelet

docs/guis/about.md

@@ -101,7 +101,7 @@ If you encounter a complaint about `Java` being too old, try using `/mcr/bin/jws
     ```bash
     javaws https://bewww.cern.ch/ap/deployments/applications/cern/lhc/lhc-app-beta-beating-omc3/PRO/BetaBeatingOMC3-Control-3t.jnlp
     ```
-    :material-arrow-right-bold: Disabling Java as it is too old and likely to be insecure. To reenable use jcontrol utility
+    :material-arrow-right-bold: Disabling Java as it is too old and likely to be insecure. To re-enable use jcontrol utility
 
 !!! success
     ```bash

docs/guis/betabeat/analysis_panel.md

@@ -50,7 +50,7 @@ These include phase (`PHASE`), frequency (`FREQ`) and amplitude (`AMP`) of the l
 The lines are multiples of the found tunes (`TUNE`) and can be identified by the two numbers in their name,
 which correspond to the multiples of the horizontal and vertical tune, respectively, using underscores to represent a minus sign;
 e.g. `PHASE1_2`, as seen in the screenshot above, corresponds to the phase of the line at frequency `Qx - 2Qy`.
-In addtion, further data from the harmonic analysis is available, such as:
+In addition, further data from the harmonic analysis is available, such as:
 
 - `TUNE`: (driven) tune
 - `NATTUNE`: natural tune (if available)
@@ -63,7 +63,7 @@ In addtion, further data from the harmonic analysis is available, such as:
 It is possible to select multiple files (++ctrl++ / ++shift++) at once, to compare the same quantities between measurements, and also multiple entries, e.g. to compare the amplitudes of different lines.
 
 !!! tip "Deselection"
-    To see the data of one plane only, one can deselect the other plane by either chosing `None` at the bottom of the list
+    To see the data of one plane only, one can deselect the other plane by either choosing `None` at the bottom of the list
     or by right-clicking into the respective list.
 
 ### Cleaning
@@ -164,7 +164,7 @@ It is possible to select multiple files (++ctrl++ / ++shift++) as well as multip
 Depending on the number of selected files and BPMs as well as the frequency resolution of the spectra, the GUI may take a few seconds to display all data.
 
 !!! tip "Deselection"
-    To see the frequency data of one plane only, one can deselect the other plane by either chosing `None` at the bottom of the list of BPMs
+    To see the frequency data of one plane only, one can deselect the other plane by either choosing `None` at the bottom of the list of BPMs
     or by right-clicking into the respective list.
 
 !!! tip "Find BPMs"
@@ -267,7 +267,7 @@ To update the natural tune in the lin-file, first activate the vertical cursors
 they will appear at their last set position or at 0 if they have not been set yet.
 
 !!! tip "Cursors for each plane"
-    If BPMs from both planes are selected, two sets of cursors will appear: blue for the horizonal spectrum and red for the vertical spectrum.
+    If BPMs from both planes are selected, two sets of cursors will appear: blue for the horizontal spectrum and red for the vertical spectrum.
     In case only one plane is selected, only one set of cursors will appear.
     To update the amount of cursors shown, select BPMs in the desired planes, then untick and re-activate the **Show** checkbox.
 

docs/guis/betabeat/beam_selection.md

@@ -42,7 +42,7 @@ Depending on your choice of `Beam` a default is already preselected for you.
 #### Folder Structure
 
 Within your selected output folder, a new folder for the current date will be created.
-Withing that folder, a folder for the selected beam/accelerator will be created.
+Within that folder, a folder for the selected beam/accelerator will be created.
 Within that folder in turn, folders for `Measurements`, `Results` and `Models` will be created.
 If any of these folders already exist, they will be used, e.g.:
 

docs/guis/betabeat/betabeatsource.md

@@ -21,7 +21,7 @@ One can compensate for this deviation in different ways, which is why there are
     | :---------------- | :------------------------------------------------------------------------------------------------------------- |
     | `get_*.out`       | The optics functions **without** compensation, from the driven excitation data.                                |
     | `get_*_free.out`  | The optics functions compensated **analytically** using an equation[^MiyamotoMeasurementCouplingRDTsACDipole]. |
-    | `get_*_free2.out` | The optics functions compensated **the other way**, see bellow.                                                |
+    | `get_*_free2.out` | The optics functions compensated **the other way**, see below.                                                |
 
     In the case of the `get_*_free2.out` files, the compensation is done differently depending on the computed quantity.
     For some quantities (for instance for $\beta$ from phase) this uses the model values, for others (for instance the coupling RDTs $f_{1001}$ and $f_{1010}$) it is a rescaling in which the model values are used *indirectly*.

docs/guis/betabeat/common_components.md

@@ -53,7 +53,7 @@ If you are using an older version than recommended, a lot of the functionality m
 features might be missing or not work with the arguments the GUI provides.
 
 The colored button and dropdown menu that follows is the **RBAC** (Role Based Access Control) menu,
-which shows you the current status of, and allows you to aquire, an access token,
+which shows you the current status of, and allows you to acquire, an access token,
 e.g. for the [creation of knobs](correction_panel.md#knob-creation).
 
 Next, in the middle of the screen, the **currently selected model** is shown.
@@ -114,7 +114,7 @@ additional logging information will be printed to the terminal.
 </figure>
 
 A "task" in the context of this GUI means the running of an external program in a separate process.
-Sometimes even multiple processes might be started consecutively in the same taks, if they are dependent on each other.
+Sometimes even multiple processes might be started consecutively in the same tasks, if they are dependent on each other.
 As the GUI is a front-end for our `python` library, the external processes are usually calls to `python` modules,
 constructed from the currently selected files and [settings](settings.md).
 The exact call can often be found in the [terminal](#terminal) or in the `command.run` files often created by th GUI in the selected output folder,
@@ -152,12 +152,12 @@ Go to the path set as [_Input Path_ in the beam selection window](beam_selection
 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_,
+This is usually the date-directory within the output folder, unless you have chosen 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).
+Go to the fill-directory of [the chosen 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),
+Go to the default OMC analysis directory of [the chosen 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

docs/guis/betabeat/defaults.md

@@ -49,7 +49,7 @@ clean.bounds=0.7     # this ratio of points needs to remain otherwise cleaning a
 ampdet.tunecut=0.05  # limit around the given tune to exclude from the BBQ tune
 ampdet.window=100    # length of the moving average window for the BBQ tune
 ampdet.outlierLimit=0.0002   # Cut on outliers around the mean
-ampdet.usePreviousBBQ=False  # Use previously extraced BBQ data if present
+ampdet.usePreviousBBQ=False  # Use previously extracted BBQ data if 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.

docs/guis/betabeat/model_creation.md

@@ -58,8 +58,8 @@ A window will open to select a time to extract the MQTs from, which default to t
         It checks in the model folder if the `extracted_mqts.str` file is present, which it updates,
         and if `job.create_model_best_knowledge.madx` exists, which is then reused to re-run.
 
-    !!! warning "Updating MQTs to re-use model"
-        It is **heavily discouraged** to update the MQTs to re-use a model later during a shift,
+    !!! warning "Updating MQTs to reuse model"
+        It is **heavily discouraged** to update the MQTs to reuse a model later during a shift,
         as it will lead to confusion if optics have already been analyzed with this model and someone tries to reproduce the results later.
         It is therefore usually better to create a new model from scratch and **only use this functionality before doing any analysis**,
         e.g. if you extracted the MQTs too early, or if you created a copy of an older model.
@@ -131,7 +131,7 @@ The value by which each variable will be changed to check the response.
 !!! note "FullResponse Task"
     The full-response creation will only start after the model is fully created and you have closed the popup-window
     asking you to load the model or not (see below).
-    By that time you can **already use the model** as if it was fully created and you **do not need to wait for this taks to finish** for the _standard_ analysis, until you want to calculate [global corrections](correction_panel.md).<br>
+    By that time you can **already use the model** as if it was fully created and you **do not need to wait for this tasks to finish** for the _standard_ analysis, until you want to calculate [global corrections](correction_panel.md).<br>
     The full-response creation is also heavily parallelized where possible, so expect a few processes to run at the same time.
 
 #### User
@@ -180,14 +180,14 @@ which are our default tunes for LHC measurements.
 #### Accelerator (LHC)
 
 - **Beam**:
-The beam is pre-defined by the accelerator choosen in the [beam selection window](beam_selection.md).
+The beam is pre-defined by the accelerator chosen in the [beam selection window](beam_selection.md).
 - **Year/Tag**:
 This field is automatically filled by the fetcher with the first layer of subfolders in the `acc-models/lhc` repository by the fetcher.
 - **Energy**:
 The energy at which the accelerator is running in GeV.
 - **Optics File**:
 The optics used for the model, which has the same name as the one used in the machine.
-The **File** dropdown is automatically filled by the fetcher with the files in the `operation/optics` folder within the choosen _year/tag_
+The **File** dropdown is automatically filled by the fetcher with the files in the `operation/optics` folder within the chosen _year/tag_
 of the `acc-models/lhc` repository.
 You can search through the list via regular expression in the **Filter** field.
 - **dpp**: The momentum deviation for the model.
@@ -217,7 +217,7 @@ In addition, this model contains also the $b_2$ errors of the main dipoles from
 This will result in additional `*_best_knowledge.dat` twiss-output files, which are used in the N-BPM method of the beta-from-phase analysis
 (see _[Langner et al. - Utilizing the N beam position monitor method for turn-by-turn optics measurements][langner2016]{target=_blank}_).
     - **$b_2$ error table**:
-      As these errors are dependend on the powering of the dipoles, you need to choose the table with the closest energy to the one you are creating the model for.
+      As these errors are dependent on the powering of the dipoles, you need to choose the table with the closest energy to the one you are creating the model for.
     - **:fontawesome-solid-triangle-exclamation:{.warning-colored} Extract MQTs**:
       As the $b_2$ errors change the tunes, you should **always also extract the MQTs** when creating the best knowledge model.
 
@@ -249,7 +249,7 @@ The **fractional tunes** are set by default to some values, that have suited us
 but as the settings of the SPS can differ quite drastically, you need to check the currently used values in the SPS multiturn application.
 
 !!! warning "Integer Tunes"
-    The **integer part of the tunes** is set from the filename of the choosen _Strength File_ (below).
+    The **integer part of the tunes** is set from the filename of the chosen _Strength File_ (below).
     To set them manually, make sure to **first select a strength file and then change the integer tunes**.
 
 #### Accelerator (SPS)
@@ -259,7 +259,7 @@ Which year to create the model for.
 This field is automatically filled by the fetcher with the first layer of subfolders in the `acc-models/sps` repository.
 - **Strength File**:
 Strength file to use.
-This field is automatically filled by fetcher with the files in the `strengths` folder within the choosen _year_ of the `acc-models/sps` repository.
+This field is automatically filled by fetcher with the files in the `strengths` folder within the chosen _year_ of the `acc-models/sps` repository.
 - **Kinetic Energy**: Activate and set the energy at which the accelerator is running in GeV, if needed for your model.
 
 ### PS Model Creation
@@ -284,7 +284,7 @@ Which year to create the model for.
 This field is automatically filled by the fetcher with the first layer of subfolders in the `acc-models/ps` repository.
 - **Scenario**:
 Operational scenario of the PS accelerator.
-This field is automatically filled by the fetcher with the content of the `scenarios` folder within the choosen _year_ of the `acc-models/ps` repository.
+This field is automatically filled by the fetcher with the content of the `scenarios` folder within the chosen _year_ of the `acc-models/ps` repository.
 - **Cycle Point**:
 Desired point in the cycle.
 This field is automatically filled by the fetcher with the content of the chosen _scenario_ folder above.
@@ -325,7 +325,7 @@ Which year to create the model for.
 This field is automatically filled by the fetcher with the first layer of subfolders in the `acc-models/psb` repository.
 - **Scenario**:
 Operational scenario of the PSBooster.
-This field is automatically filled by the fetcher with the content of the `scenarios` folder within the choosen _year_ of the `acc-models/psb` repository.
+This field is automatically filled by the fetcher with the content of the `scenarios` folder within the chosen _year_ of the `acc-models/psb` repository.
 - **Cycle Point**:
 Desired point in the cycle.
 This field is automatically filled by the fetcher with the content of the chosen _scenario_ folder above.

docs/guis/betabeat/settings.md

@@ -33,7 +33,7 @@ There is some general behaviour, that is true for all settings-tabs:
   Entries in the file, that are not recognized as settings will be ignored.
 
 !!! info "Some Background on the Internals"
-    To "apply" settings simply means that the current values in the UI are assinged to the corresponding settings class,
+    To "apply" settings simply means that the current values in the UI are assigned to the corresponding settings class,
     each an internal representation of a settings tab,
     which is used to persistently store the settings in memory and pass them between different parts of the application.
     To "reset" the settings, the stored values are reloaded from this internal representation to the UI.
@@ -80,7 +80,7 @@ This is in contrast to the other settings tabs, which control the settings passe
   If active, the GUI will run the `python` script with the `-d` flag, which initializes the logging level in our scripts automatically to `DEBUG`.
 
 - **Use Server for Analysis**:
-  When set, all `python` tasks requireing lots of memory and processing power (e.g. `hole-in-one` for `harpy` and `optics`) will be run on that server.
+  When set, all `python` tasks requiring lots of memory and processing power (e.g. `hole-in-one` for `harpy` and `optics`) will be run on that server.
   If you click the ++"Test"++ button, file creation and reading of the created files from the local machine will be tested and you will be prompted with the results after a few seconds.
 
 - **Always use Server**:
@@ -91,7 +91,7 @@ This is in contrast to the other settings tabs, which control the settings passe
   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 opting to run the `optics analysis` directly from the BPM-Panel with _"combine analysis"_ **activated**,
-  the `harpy` analysis of the selected files will be run sequentially per file, as it is not explicitely parallelized on the python side.
+  the `harpy` analysis of the selected files will be run sequentially per file, as it is not explicitly parallelized on the python side.
 
 ## Tunes Tab
 
@@ -140,7 +140,7 @@ The fields are non-editable when it does not make sense in the current settings
   Otherwise the main tune is defined as the highest peak in the spectrum around the tunes given in the first row ± the tolerance.
 
 - **Clean Limit**:
-  When cleaning is active, BPM outliers are detemined as those that are further away than others from the average.
+  When cleaning is active, BPM outliers are determined as those that are further away than others from the average.
   This limit sets a hard border to the cleaning, where **outliers closer than the given limit to the average tune will not be removed**.
 
 - **Tolerance**:
@@ -375,7 +375,7 @@ introduced by the AC-Dipole and if they are not found in the data, the optics an
   Default: `False`.
 
 - **Calculate only coupling**:
-  When active, skips most of the optics calcualtions and calculates only phases and coupling RDTs.
+  When active, skips most of the optics calculations and calculates only phases and coupling RDTs.
   Useful for quick analysis or machines that do not support (e.g. not enough BPMs) some of the other analysis methods.
   Default: `False`.
 
@@ -471,7 +471,7 @@ which is the `python`-internal representation of the accelerator and its setting
     In `model/settings`:
 
     - add a **descriptive attritbute** to the respective settings class.
-    - add your vlaue to the **constructor** of the class, with default values.
+    - add your value to the **constructor** of the class, with default values.
     - add your value to the **copy-constructor** of the class.
     - add a nice **tooltip** to the label (e.g. the help text from the corresponding `python` argument).
     - use `getProperty()` to automatically **extract** the value from the property file in a unified way and set the attribute on the class.