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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.
A summary of key commands may be obtained using the Help -> Aperture Def Help menu on the menubar.
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To start this process, in the Extraction preferences, select Object Finding: Interactive/User Defined and Extraction Method: Optimal. Then, as in the boxcar case FIREHOSE will solve for the wavelength map and present you with a first-pass sky subtracted frame as shown here:
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 wavelengths run vertically in FIREHOSE frames, this means you need to set the bottom and top of the bounding region.
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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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 
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.
If this plot does not look crazy, then you can hit "q" and then the optimal extraction begins. For this sequence, FIREHOSE still makes local adjustments to the sky model during extraction, but it does not simultaneously update its estimate of the object profile model - i.e. it keeps the one that you fit.
PLEASE KEEP IN MIND: When you do interactive profile fitting like this, the extracted errors are only as good as your object profile model. Check the error vector that comes out when you finish combining your spectra to 1D to see that they are sensible!