# Initial atmospec development work

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#### Details

• Type: Story
• Status: Done
• Resolution: Done
• Fix Version/s: None
• Component/s:
• Labels:
None
• Story Points:
40
• Team:
Data Release Production

#### Description

Write a hacky, zeroth order version of the pipeline so that we have some skeleton tasks and structures in place to iterate on.

This should probably be done on a user branch, but I wanted to have a ticket number for this work to save git hassles later on as this will touch more than just atmospec.

This will initially be pretty hacky in places and probably not adhere to all standards, but will be tidied up before review.

Checklist/to-do list/steps in Augustin's pipeline:

 Prepare Image:  Load image from disk  Subtract overscan and trim & assemble   Initial ISR Step  Load the dark by filename  Scale the dark by exposure time and subtract  (you don not want to see the details of this!)   Source extraction (using SExtractor):  Find the objects and centroids   Load SExtractor catalog   Process catalog to find the primary object  return the x,y of the brightest, roundest object's centroid   Calculate the spectrum's bounding box, depending on dispersion direction and the order used  Dispersion direction is either just x or y, not arbitrary angles yet  Will need extending for arbitrary angles   Secondary ISR:  Load masks from disk if masking  removal of periodic pattern on chip  Create initial dispersion relation  Apply initial flatfielding  Find and interpolate over cosmics   Extraction (choice between three methods:)  Spectral extraction method 1:  Calculate row-wise mean and sigma of background and subtract  Row-wise, calculate:  aperture flux  PSF 1D-Gaussian flux  Moffat flux  Gauss-Moffat Flux  Voigt flux    Spectral extraction method 2:  Calculate row-wise sum for aperture flux without subtracting background)  Fit 1D Gaus for PSF flux (again, without bgSub, and without pedestal in fit function)  Same for Voigt fit (no bgSub here either)    Spectral extraction method 3 (two pass method):  1st pass: fixed aperture, no centroid, meaning that:  Per row:  Fit 1D Gaus for PSF flux (again, without bgSub, and without pedestal in fit function)    Between passes, fit the row-wise Gaussian's parameters with linear and quadratics functions describing the position and width of them as a function of row number i.e. position in the spectrum, respectively  2nd pass: applying a variable aperture, using the 1D centroid and 1D sigma provided, meaning that:  Per row:  Regular aperture flux summing (still without bgSub I think)  aperture is centered at the row's centroid, and 6 sigma around it  fit Gaussian over a very narrow range (120-180 pixels) up spectrum   Post-extraction:   Reflatfield   Find lines in spectrum   Match to known lines   Refine the dispersion relation calculation

#### Activity

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John Swinbank added a comment -

We discussed this at our meeting of 2018-12-10. We agreed that it was appropriate to have a “big bang” ticket for bootstrapping initial atmospec development, but that it'd be helpful to expand this ticket with a checklist of work that it includes.

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John Swinbank added a comment - We discussed this at our meeting of 2018-12-10. We agreed that it was appropriate to have a “big bang” ticket for bootstrapping initial atmospec development, but that it'd be helpful to expand this ticket with a checklist of work that it includes.

#### People

Assignee:
Merlin Fisher-Levine
Reporter:
Merlin Fisher-Levine
Watchers:
John Swinbank, Merlin Fisher-Levine