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By selecting "Interactive / User Defined" on the Object Finding section of the Extraction preferences, you will be presented with a GUI to aid in setting extraction parameters as the pipeline runs. Depending on the type of data being used, you may set an object trace center and aperture for simple boxcar style extraction, or you may fit an object profile to a particular emission line and use this as the weighting function for optimal extraction.
The selection of boxcar versus optimal is an either/or choice, you can't run both together. But they are launched from the same GUI. The PRELIMINARIES section below describes this GUI and then you can refer to the relevant section for your particular choice of extraction method.
PRELIMINARIES
For each exposure, FIREHOSE first performs a crude first-pass sky subtraction to assist in locating the object in the 2D frame. A display GUI will pop up showing the sky-subtracted frame. Below I show an example of this GUI for an object showing a single emission line near the center of the display but no continuum.
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A summary of key commands may be obtained using the Help -> Aperture Def Help menu on the menubar.
SET APERTURES FOR BOXCAR EXTRACTION (see below for interactive object profile fitting/optimal extraction)
To define the trace location using the GUI, center the cursor over the emission line (or any location on the image) and press the space bar. A cross will appear to indicate the location of your choice. You may define many crosses and the software will use the median spatial location for the aperture.
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You may return to the aperture dialog box to readjust your values if you wish. When you are happy, click "done" or type "q" to exit the aperture definition GUI and return to the pipeline. Another xatv GUI may pop up immediately after to confirm your object placement; you can ignore this instance and quit out to proceed with the object extraction.
PROFILE FITTING FOR OPTIMAL EXTRACTION
As an alternative to boxcar/aperture extraction, it is also possible to trim a small region around an emission line to fit a spatial profile to the object for optimal extraction. This feature is in the beta+ stage but appears to work stably. At present, one can only fit to the profile of a single wavelength region from a single order (i.e. around a bright emission line like H alpha). The profile fit in this way is then applied to the entire spectrum. It is not possible to fit profiles on an order-by-order individual basis (it would require some extreme patience anyway).
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In this case I have zoomed in to the line of interest, an H alpha profile of a z = 1.7 galaxy. Now, rather than defining the center of the aperture in spatial coordinates, you must define the bounds of the wavelength region of interest where you want to fit the profile. Since Since wavelengths run vertically in FIREHOSE frames, this means you need to set the bottom and top of the bounding region. . You do this by hovering the mouse over the desired bounds and pressing capital "B" and "T". The display will show black lines indicating where it interpreted your top and bottom bounds to be drawn.
Once you have set the top and bottom bounds, the software will sum up the flux from pixels in that wavelength region and present the normalized pixel profile in a new window, where you can interactively fit a parametric model to the pixel values:
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There is a small help menu indicating the range of commands one may use to control the fit. Common options are to delete/undelete bad points (right mouse button) force a point to be added in a desired location (left mouse button), increase the fit order ('u') or decrease the fit order ('d'). You can also select a particular region for fitting using the combination "s-s" on the left and right bounds of the region of interest. When you are satisfied with the fit, press 'q' or click "done" and the software will return you to the image GUI. For reasons I don't understand, the colormap gets messed up when you do this, but do not worry, this is normal.
Press "q" again in the image GUI to move on to extraction. The software will then create a 2D profile image based on the fit you just completed. It will present you with another view of the 2D crude-sky-subtraction, this time showing the profile peak position, and the +/- 1 * FWHM boundary.
If your object is close to the edge of the slit (as in the example shown), one of the bounds sometimes lies outside of the order: do not worry. This aperture is only used to run a quick boxcar prior to optimal extraction, for determining in what sequence the individual orders will be extracted. The optimal extraction will not use any "aperture" per se, it only uses the profile weighting function that you have specified, and does not extend outside of the slit. Generally, if the center trace lands on the middle of your object, you are good to go.
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