calcos 3.0

Calibration software for COS (Cosmic Origins Spectrograph)

Release Notes
-------------

This addresses the following PR:

PR#79304 CALCOS should implement two-zone extraction

CALCOS was upgraded to Version 3.0 to support the move of the COS FUV
channel to Lifetime Position 3. This move involves changing the aperture
block position so that the spectrum will be located approximately x
pixels (y arcsec) below its location during Lifetime Position 1. As a
result of this move, some of the gain sagged regions from LP1 will be
close to the edge of the extraction aperture at LP3.

CALCOS Version 3.0 addresses this by splitting the extraction region
into two parts: the inner region, where most of the flux is, will be where
DQ flags are propagated to the output extracted spectrum. The outer region,
containing a much smaller fraction of the flux, will contribute to the
total flux measurement, but its DQ flags will be ignored. This 'two zone'
extraction algorithm involves several significant changes to CALCOS.

Most of the significant changes are confined to extract.py and the new
module, trace.py. The former now has two extractSegment methods:
extractSegmentBoxcar and extractSegmentTwozone, with all of the new
extraction algorithms in the latter function.

The new module trace.py includes code to perform two new calibration
steps: trace correction (trcecorr) and profile alignment (algncorr). In
the trace correction step, the 1-d profile of the centroid of the spectrum
is corrected for its up-and-down wiggles to make a horizontal spectrum.
In the profile alignment step, the centroid of this spectrum in the cross
dispersion direction is measured and compared to the centroid of a high
signal to noise template, and shifted to make the science data spectrum and
reference profile have the same centroid. This ensures that the (narrower)
extraction regions are still centered on the spectrum.

Modules changed:

Setup.cfg:

Version and author(s) changed

lib/calcos/airglow.py:

New module to ensure that the regions around airglow lines are not included
in the profile alignment centroid calculations.

lib/calcos/calcosparam.py:

Added sp_err_X to list of segment-specific keywords.
Added MissingColumnError exception.

lib/calcos/calcos.py:

Added code to deal with 3 new reference file types: TRACETAB, PROFTAB and
TWOZXTAB.

lib/calcos/concurrent.py:

New calling sequence for extract.extractCorrtag

lib/calcos/extract.py:

Major changes. extractSegment() is now split into extractSegmentBoxcar()
and extractSegmentTwozone(). Calling sequence to extractSegmentBoxcar is
different from extractSegment because of the new columns added to the x1d
file. extractSegmentTwoZone contains the code to do the two-zone extraction,
and uses the following new functions:
getProfileCentroid()
getBackgroundCenters()
getBackgroundRegion()
getBackground()
getPercentiles()
NormalizeProfile()
getPercentileVectors()
bitwise_or_vector()
next_power_of_two()
remove_unwanted_columns()

lib/calcos/fpavg.py:

Remove added columns from x1dsum files.

lib/calcos/getinfo.py:

Added new correction steps (trcecorr, algncorr) and reference files
(tracetab, proftab, twozxtab) to getSwitchValues() and getRefFileNames()

lib/calcos/timetag.py:

Added three new functions to do trace correction and profile alignment:
createTraceMask()
doTraceCorr()
doProfileAlignmentCorr()

lib/calcos/trace.py:

New module that holds all the code for trace correction and alignment
correction. Includes functions
def doTrace()
def getTrace()
def cleanTrace()
def applyTrace()
def doProfileAlignment()
def rebinData()
def rebinCounts()
def maskAirglowLines()
def applyWavelengthLimits()
def getWavelengthLimits()
def getGoodRows()
def getRegions()
def getGoodColumns()
def getScienceCentroid()
def getBackground()
def getCentroid()
def getCentroidError()
def calculateCentroidError()
def getReferenceBackground()
def getReferenceCentroid()
def applyOffset()
def updateTraceKeywords()