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some josh comments
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docs/guis/betabeat/analysis_panel.md

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@@ -85,6 +85,10 @@ which trigger the python [`linfile_clean` script][omc3_linfile_clean]{target=_bl
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You can therefore specify to **keep these BPMs** in the [GUI Cleaning section of the Cleaning Settings Tab](settings.md#gui-cleaning) and they will be kept,
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even if they are outside the given [cut-offs](#clean) or identified as [outliers](#auto-clean).
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!!! tip "Always remove BPMs"
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If BPMs show up regularly as outliers in the data, independent of machine configuration, it is likely that they are [faulty BPMs][bad_bpms].
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You can specify to **always clean these BPMs** during the cleaning of the data in the `harpy` analysis via the `Bad BPMs` field in the [Cleaning Settings Tab](settings.md#cleaning-tab).
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#### Clean
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=== "Before Cleaning"
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#### Auto Clean
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A more automated cleaning approach can be utilized with the help of the _outlier filter_ (see Section 3.2.3 in [Malina2018][malina2018]{target=_blank}
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or Section II.E.1 in [Dilly2023][dilly2023]{target=_blank}), which iteratively removes points in the tails of the data until the distribution of the remaining data is close to a normal distribution.
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A more automated cleaning approach can be utilized with the help of the _outlier filter_
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(see Section 3.2.3 in [Malina2018][malina2018]
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or Section II.E.1 in [Dilly2023][dilly2023]), which iteratively removes points in the tails of the data until the distribution of the remaining data is close to a normal distribution.
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The _limit_ parameter defines a "save zone" in standard deviations around the mean, in which data will not be removed (default: `0.0`, i.e. any datapoint could be removed).
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This cleaning can be run by simply pressing the ++"Auto"++{.red-gui-button} button and is then applied to **all data currently shown in the chart**, individually per column, plane and `sdds`-file.
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Use the controls at the bottom left of the panel for the additional functionality, which is described below.
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### Resonance Lines
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<figure>
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Use ++"Add Line"++{.green-gui-button} to add a new line based on your input to the table and ++"Remove"++{.red-gui-button} to remove the currently selected line.
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The lines in the charts will only update after clicking ++"Approve"++.
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=== "Natural Tune Line"
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<figure>
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Which also means, that no matter in which plane you have selected a BPM - if it has a horizontal and a vertical spectrum they will both be plotted.
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- _"Combine Plots by BPMs"_: Will plot all selected BPMs into the same plots in the same file, with the BPM name in the legend.
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If deactivated, there will be separate files per BPM with the BPM name in the filename.
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- _"Combine Plots by Measurements"_: Will plot all selected Mesurements into the same plots in the same file, with the Measurement name in the legend.
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- _"Combine Plots by Measurements"_: Will plot all selected Measurements into the same plots in the same file, with the Measurement name in the legend.
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If deactivated, there will be separate files per Measurement with the Measurement name in the filename.
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- Having both _"BPMs"_ and _"Measurements"_ activated will therefore lead to a single output file, with a chart for each plane and a combination of BPM and Measurement names as legend.
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- Having both _"BPMs"_ and _"Measurements"_ deactivated will lead to `N = No. of selected BPMs x No. of selected Measurements` files, containing two charts for the planes with each showing only a single spectrum.

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