Interactive Dark Current Subtraction 

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Invoking the Interactive Tool 

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The following Widget will pop-up (the plot area will be empty; button 'LW3' has been hit in the example below):
 

A Description of the User Interface 

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1. two sets of red points: this is the dark current measurement  done at the beginning of the AOT; remember that the second set of red points IS NOT GOING TO BE USED in the processing as the detectors at this stage are still recovering (check that the signal is decreasing with time) due to the strong signal received from the Illuminators.
2. another set of red points may appear if the Illuminator Flashes have been done in the OLD scheme. This set is not used in the processing (see previous point).
3. a set of white points: these are the actual scientific data. In the case shown above they come from an L01 AOT ; the time series of scans accumulated is clearly discernible. Remember that at this stage the data is not yet calibrated so each scan resembles the instrument transmission profile (referred to as Relative Spectral Response Function - RSRF) for that detector.
4. another two sets of red points: this is the DC measurement done at the end of the AOT (see point 1).
5. a final set of red points (see point 2).

Below the plot area the following groups of buttons are visible from left to right:

• The 10 LWS detectors buttons
• Dark measurements buttons: there is 1 button for each dark measurement performed in the AOT. Aside each of these buttons there is a text field which will show the estimated DC value (see below), and where numbers cna be inserted directly by hand (remember to hit Return); further on the right there are other text fields (again, 1 for each DC measurement) showing the DC values estimated automatically by the OLP.
• Masking buttons: pressing one of them make the right button of the mouse active (click and drag) to select portions of the data to be masked/unmasked. In the first case data within the selected area will turn to blue and will be ignored in further processing; in the second case data previously masked are brought back to white colour and become again available for processing.
• Operations buttons: a series of buttons performing actions which will be explained in detaile in the following and providing options for the temporal interpolation of the DC and its subtraction from the data.

The DC estimate & subtraction Cookbook 

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• Select one detector by clicking on one of the detector buttons; a plot similar to the one shown in the example above should appear.
• Select the 'Dark # n' button (likely starting from the first): the button is a 'pull down' menu and two possibilities are available and should be selected in sequence:
• 'Zoom Flash' will cause to enlarge the region of the DC measurement selected; the plot is shown in linear scales to be able to include also the negative points. The points that will be averaged to produce the DC estimate are the red ones at the extreme left of the plot, so the user will want to zoom more on that region using the left button of the mouse. It is time now to check that bad points (such as 0s or  clear outlier points like glitch remnants) are not included in the DC estimate; to get rid of those points use the button in the 'Masking Options' section. Some thing like this should be seen:


 
• 'Estimate Dark' will perform a n-sigma clipped median averaging of the individual measurements (red points), print,the resulting DC photocurrent in the area left of the 'Dark # n' button, in the text area at the bottom of the widget ('greyed' at this stage) and on the terminal window. A white dashed line is overplotted representing the averaged value and a small widget pops-up asking how to proceed further:
• 'I am happy with that' accept that value: click it if you are happy with the result.
• 'I want to change clip level': you are not satisfied with the estimate and want to try again the n-sigma median averaging but with a different n value. Just input a new n value in the small text field and click the button: the average is soon recomputed and the new value overplotted.
• 'Fix it by hand': there is no way of getting what you think is the correct value (use a grain of salt and a lot of common sense) via averaging so you want to set a particular value by hand. Click that button and then click again on the plot with the right button of the mouse just at the Y position you think is correct.
• 'Do not accept' if you are not sure how to proceed and you want to think a little bit about it.

The user can also insert his own estimate of dark current by hand directly in the relevant text field under 'Dark Measures' ; remember to hit 'return' button

Everything done till now should be repeated for each DC measurement (each 'Dark #n' button) and for each detector. In some cases the user may want, for a particular detector and DC measurement, to adopt the DC value that OLP has automatically estimated; this can be done by clicking on the 'left arrow' button in the 'Dark Measures' section (see below)



Note that apart from the 'Quit' button, all other buttons in the 'Operations' area will stay inactive until DC values have been estimated for each dark measure and for each detector. When 'Operations' buttons are active, it is time to do the temporal interpolation, for each detector, of the previously determined DC values to determine the DC for each 'science' data point.
 

• Click on detector button to select a particular detector (you have to do it for all detectors): the complete data time series is shown along with adopted DC values in the proper text fields.
• There are two ways the user can interpolate between estimated DC values: linear interpolation or polynomial fit.
• 'Linear interpolation' button is a pull-down menu where the user can select among the four options described below
• 'Use all darks' will use all DC values estimated;
• 'Use first dark only' will assume that dark current is costant throughout the whole AOT and equal to the first estimated DC value;
• 'Use last dark only' will assume that dark current is costant throughout the whole AOT and equal to the last estimated DC value;
• 'Use average of darks' will assume that dark current is costant throughout the whole AOT and equal to the arithmetic average of all estimated DC values (which is what is automatically done by OLP); the user is strongly encouraged to use this option unless there are good reasons to think the DC is varying throughout the AOT.
• 'Polynomial Fit'  button is a pull-down menu where the user can select 1^st, 2^nd or 3^rd order polynomial fit to all estimated DC values.


An option that has to be used with lot of caution is the possibility of 'adding points' to help fancy DC interpolation if the user has serious reasons to believe that the dark current is doing strange things during the AOT. Clicking on 'Add Points' enables the user to set an additional point on the plot by clicking with the right button of the mouse (a red cross appears); if the user is not satisfied with the points added he can get rid of them by clicking on 'Clear extra points' . Various attempts can be done and they all will be overplotted:


 
 

• When the user is happy with the interpolated dark current hit 'Subtract!'  and the DC-subtracted data will be overplotted in yellow (multiple subtract actions will have no effect); note that the last interpolation done is subtracted, although many attempts may still be visible on the plot. Hitting 'Subtract' makes no harm as you can always make another interpolation and subtract again: the 'Subtract' button always acts on the original data (but it does not overwrites them).

 

 
 
 
 
 
 
 
 
 



Note: in case of a faint source or of a Fabry-Perot observation, the DC values will be comparable to the source signal and, as a result, the DC-subtracted spectrum (yellow points) will be very faint and possibly off-scale: use the 'Zoom' button to increase the dynamical range of the Y axis so that the yellow points can be seen.

When the DC is subtracted, a label will appear on the detector button pertinent to the data under analysis ('LW3' in the present case) to remind the user that DC has been subtracted for that detector (something which does not prevent the user to do it again, see above); the label is different, according to the type of dark current that has been interpolated, according to the following table:
 
 

Type of Interpolation Performed	Label
Linear, using all Darks (including extra points, if any)	L1
Linear, using first dark only (i.e. DC constant and equal to the first measured  value)	L2
Linear, using last dark only (i.e. DC constant and equal to the last measured  value)	L3
Linear, using the average of first and last darks (i.e. DC constant and equal to the arithmetic average of first and last measured dark currents)	L4
1st order Polynomial interpolation (using all dark current values, including extra points, if any)	P1
2nd order Polynomial interpolation (using all dark current values, including extra points, if any)	P2
3rd order Polynomial interpolation (using all dark current values, including extra points, if any)	P3


 

• When dark current has been interpolated and subtracted for all 10 detectors the user click 'Write new LSPD and Exit'. A new LSPD file is written on the disk (same location of the input files as specified by the 'dir' variable in the calling command) with a '_newdarks' appended. The user can go on for further processing.