# Force baseline correction

## Description

When the optical traps move close together, one trap starts pulling on the bead in the other trap, which results in a
'baseline force'. In Bluelake, the baseline force can be subtracted from the force, while collecting data. First, the
forces `HF/Force 1x` and `HF/Force 2x` are recorded for a given time interval to obtain the baseline. Next, Bluelake
fits a 7th degree polynomial to the resulting force signal. When the baseline correction is applied, the channels
`HF/Corrected Force 1x` and `HF/Corrected Force 2x` show the force with the baseline subtracted, i.e. 'corrected'.

##  Usage

To perform force baseline correction, the same steps for doing an `FDCurve` measurement are performed. This means:
* Beads should be captured
* Templates applied
* The force calibrated

For measuring the baseline, follow these steps:
1. Select `Trap 1` in Bluelake
2. Navigate to the `FDCurve` section
3. Enter parameters (start/end position, speed) for measuring the baseline, as is done for a regular `FDCurve`
4. Click one of the directional buttons next to 'Measure baseline'

### Popup

When the force baseline has been measured, a popup appears showing tabs for each of the force channels. Each tab
displays a graph showing the Force vs the Trap 1X positions. The graph displays two plots:
* The original Force vs Trap data as a scatter plot
* The corrected Force vs Trap data as a line plot

The popup presents 3 options:
* Apply - Subtract the force baseline from the force and display the results in the channels `Corrected Force nx`. The
  baseline can be viewed by clicking `View` in the `FDCurve` section. The baseline correction can be undone by clicking
  `Discard Correction`
* Cancel - Discard the measurement, no baseline correction is applied
* Redo - Redo the measurement of the baseline using the same parameters

## FD widget

As with the `FDCurve` feature, the corrected force channels are available for viewing the plots of a tether in the
`FDCurve` Item on the Data Viewer screen. The desired correction channel can be selected the same way as the original
force channels using the drop down list.

## Metadata

The polynomial coefficients for the current correction can be accessed in the metadata of the exported `FDCurve` data.
Note: Discarding a correction also erases the coefficients.

## Troubleshooting

### Issue

The motion controls for force baseline correction are not available on the UI.

### Possible solution

Make sure the Tap 1 is selected. The controls are not visible when any other trap is selected.