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HISTORY.txt

Cosmos 2.21 - released 8-29-14
- updated defineobs (and defineobs.py) to accommodate new LDSS3-C data
- updated opticdef.dat with newer ALIGNROT values for some dispersers
- added new dewar definition files for LDSS3-C
- updated some dewar offset files
- updated HeNeAr line lists with redder lines
- updated example obsdef files for newer data
- updated display8.cl to print warnings
- added shortcut keys to viewspectra
- added new sample IMACS f/2 data
- updated documentation

Cosmos 2.20 - released 7-2-14
- updated documentation, including consolidating available downloads
into a Downloads page
- reverted defineobs to previous format which asks for the observation
date and has the basic camera choices for IMACS
- added simple command-line version of defineobs called defineobs.py
written in Python and requires no additional dependencies
- fixed bug in extract-2dspec when running on a single longslit
- fixed bug in adjust-map when running through a second pass
- added new parameters to subsky:
edge2 number of rows to exclude for other slit edge
objshift number of pixels to shift object position by
- added new optional flags for subsky:
-o <object_id> run subsky only on <object>
-r load previous sky-subtracted spectra
-p <par_file> use <par_file>.par instead of subsky.par
- fixed issue with various programs reading bias-subtracted frames
- fixed issues when compiling under Mac OS X 10.9 (Mavericks)
- extract-2dspec and sumspec now preserve more of the original header
information

Cosmos 2.19 - released 4-26-13
- important bug fixes and improvements for longslit data
- fixed bug in extract-2dspec so that 'edge' parameter now works
- fixed bugs in defineobs that arise when loading an obsdef file
- updated biasflat so that the gain values are no longer input by user
- corrected slit width in longslit SMF files

Cosmos 2.18 - released 9-24-12
- updated files and programs to accommodate new camera at f/4
- fixed bug in main programs that arises when long paths are stored
in COSMOS_IMAGE_DIR and COSMOS_PAR_DIR
- updated defineobs to no longer ask for a date, but have all the
dewar choices under the camera drop-down menu; updated defineobs.html
documentation to reflect these changes

Cosmos 2.17 - released 3-7-12
- added Makefile-ldss3.Mac-Intel for building ldss3-pattern on Macs
running Mac OS X 10.6.x and later
- updated Makefile.x86_64 for Fedora 13 and later
- fixed bug in adjust-offset that affected some of the dewoff files
- updated documentation with additional tips for installing COSMOS on
Mac OS X 10.6.x (Snow Leopard) and later, and on Fedora 13 or later
- updated Running.html (Installing and running COSMOS) and FAQ.html
(Frequently Asked Questions) documentation pages
- updated default .obsdef files in $COSMOS_HOME/examples/obsdef to have
D_ALIGNROT also, to be consistent with what defineobs outputs

Cosmos 2.16 - released 7-2-10
- updated defineobs GUI to enable the user to edit the "Disperser
Misalignment" (D_ALIGNROT)
- updated align-mask to warn users if more than 3 lines are used in the
input line list file
- updated Cookbook to include another step of spot-checking the features
before proceeding with align-mask
- updated all Makefiles so that the Fortran compiler can be edited within
the Makefile for compiling the libraries

Cosmos 2.15 - released 3-5-10
- updated align-mask to be compatible with data sets with less than 8 chips
- updated map-spectra to specify number of chips being read in
- updated Sflats and subsky for smaller data sets
- included log file of session run with IMACS_sc sample data to
supplement Cookbook
- updated Cookbook, FAQ documentation pages

Cosmos 2.14 - released 1-29-10
- updated Makefile.Mac-Intel for building Cosmos on Mac OS X 10.6
(Snow Leopard)
- added parameter in align-mask.par which gives the ability to modify the
PGPLOT window size
- corrected uninitialized array problem in adjust-map
- updated documentation to include tips for compiling your own binaries
on Mac OS X 10.6 (Snow Leopard)

Cosmos 2.13 - released 6-15-09
- new fp2ccd and E2V dewdef files added to replace the preliminary files in
the 2.12 release
- reduced the incidence of numerical errors in adjust-map

Cosmos 2.12 - released 2-25-2009
- corrected the header output for logarithmic wavelength binning (CDELT1)
for extract-2dspec

Cosmos 2.11 - released 2-23-09
- added support for the red 300 line grism
- added support for D_ALIGNROT for all the IMACS grisms
- fixed a sign error with the zeroth and second moment calculations
in adjust-map for Xdisper = 0 in chips 5-8

Cosmos 2.10 - released 7-31-08
- added E2V dewdef
- added corrections for the N&S grism rotation
- added line-curvature fitting to adjust-map, now works with longslit data
- added option to run subsky without sky subtraction
- added robust clipping to align-mask
- added SMF files for standard longslit masks for LDSS3
- added Makefile for 64-bit architectures
- fixed pointer array issues with 64-bit architectures
- fixed binning in stitch
- fixed missing header keyword datasec in stitch
- fixed compiler warnings for missing include file string.h in align-mask.c
apertures.c badorders.c cos_futils.c ifu-image.c map-spectra.c mosaic.c
and spectral-lines.c


Cosmos 2.08 - released 12-19-07
- added MOE2 functionality
- fixed bug with CFITSIO3
- added object information in the adjust-map plots
- added linelists for MOE and MOE2
- temporary fix for spectral-map and long linelists
- delayed release of FFTW3 compatibility for ldss3-pattern
due to performance issues
- fixed issue with Makefiles needing spaces before backslashes that
are continuing commands onto the next line


Cosmos 2.06 - released 8-23-07
- added new program spec2big, converts from extensions to equispec format
- added new program ldss3-pattern, removes pattern noise from LDSS3 data
- improvements in performance for ldss3-pattern
- added Makefiles for ldss3-pattern.
- changed behavior of logarithmic binning in extract-2dspec
- changed headers for extract-2dspec and sumspec to standard FITS headers
- re-added histogram mode to adjust-map in order to distinguish between
slits better
- fixed bug with adjust-map for a rare failure mode, where fit
is not calculated because of insufficient data
- fixed bug with stitch incorrectly displaying the wrong size for the
header keyword datasec.
- added the SMF file for the IMACS center-field slit mask.
- added SMF files for the LDSS3 standard long slit masks.
- added Makefile for Intel Macs.
- updated FAQ documentation
- added documentation on creating and modifying dewoff files.



Cosmos 2.04 - released 12-8-06
- programs modified to reduce MOE data
- bug in process-2spec corrected
- new fitting procedure in adjust-map
- bug fixes in extract-2dspec. Additional option for adjusting scale
- new program badorders
- programs modified to permit unequal x,y binning
- display8 modified to handle 2x2 and 4x4 binned data and missing chips
- small change in map-spectra error handling
- correct bug in handling of tilted slits in adjust-map
- add option to adjust-map to specify name of new map file
- Sflats bugfixes



Cosmos 2.02-p3-b9 - released 7-27-06:
adjust-map.c:
- added histogram mode in order to distinguish between slits better
(deprecated in 2.04).



Cosmos 2.02-p3-b8 - released 7-6-06
adjust-map.c:
- fixed bug with various wavelength ranges providing different fits,
it now checks the map for the wavelength range to use.



Cosmos 2.02-p3-b7 - released 6-22-06
Makefile.linux:
- fixed issue with Makefile not being generic enough.

adjust-map.c:
- fixed bug with slits on the edge not being included.



Cosmos 2.02-p3-b6 - released 6-1-06
adjust-map.c:
- fixed bug with over-fitting He Ne Ar lines, filters out lines that are
outside of wavelength range

extract-2dspec.c:
- fixed star trace problem for 2x2 binned data



Cosmos 2.02-p3-b5 - released 5-9-06
extract-2dspec.c:
- fixed star trace problem and scale and rotation issues

sumspec.par:
- updated to include the missing parameters "iterations" and "both"

sumspec.html:
- updated to Gus's new version of documentation describing the new parameters

biasflat.c:
- fixed header issue in which biasflat would bomb if the header was a non-
standard length (i.e. spaces in the header)

subsky.c:
- added precautionary measure with the header in case biasflat was not
used to fix the non-standard header



Cosmos 2.02-p3-b4 - released 4-14-06
subsky.c:
- fixed bad pixel map for 2x2 binned data
- fixed error the sky subtraction only fitting half-way across the chips



Cosmos 2.02-p3-b3 - released 4-12-06
adjust-map.c:
- updated the clipping algorithm such that:
(1) lines culled out of the fit are not permanently culled from
subsequent iterations (we were losing lines off the ends of the
spectra that satisfied the fit of those subsequent iterations)
(2) when there are >5 lines we use a STDEV = 1.49*MAD
- added output file for STDEV values for each slit
- added plotting of spacial and wavelength fits to postscript file

defineobs:
- added IMACS_grism_150 to the list of grisms available in f/2

Sflats.c:
- fixed bad pixel map for 2x2 binned data
- fixed error with chips 1-4 with 2x2 binned data, the normalized flats
stretched only half-way across the chips

extract-2dspec.c:
- fixed field rotation



Cosmos 2.02-p3 - released 2-7-06
- spectral-map modified to support tilted slits
- documentation of sumspec updated
- bugfix to handling of flat files in process-2spec
- small adjustments to chip positions in SITE2.dewdef
- bugfix in mosaic positions in apertures, spectral-lines,spectral-map
- correct extract-2dspec for chip offset in normal orientation IMACS spectra.
Add additional option for adjusting individual spectrum offsets
- correct Sflats for normalization error when multiple flat files
- modify include directory and Makefile to force fitsio.h and fitsio2.h to
be local versions. documentation on building COSMOS modified
- dewoff file for SC150g_NS added
- sumspec modified to improve CR rejection



Cosmos 2.02-p2 - released 1-20-06
- correct bug in extract-2dspec when alignment method set to "none"
- change web pages for extract-2dspec and map-spectra to emphasize need to
map alignment holes if stars are to be used in extract-2dspec alignment
step
- bug fix to process-2spec
- correct bug in extract-2dspec affecting slit position of spectra for IMACS
Normal orientation
- correct omission of extract-2dspec from Makefile.Mac



Cosmos 2.02-p1 - released 1-17-06
- correct bug in viewspectra affecting reading of parameter files
- add check to Sflats and subsky for incorrect bad pixel locations in
badpix files
- add check to subsky for bad map files
- error in cosmos2-setup corrected
- errors in process-2spec corrected
- dewoff file for SC600g_NS added
- SITE2.badpix added
- web page for installation updated to include patches



Cosmos 2.02 - released 1-16-06
- revisions to process-2spec, sumspec.par, cosmos2-setup



Cosmos 2.0 - released 8-3-05
Parameter files:
- the parameter file directory may now be located anywhere. Its location is
specified by an environment variable COSMOS_PAR_DIR.
- The parameter files of some programs have changed, with new and renamed
parameters.

map files and dewar definition files:
- now include several additional items used by some programs.
- addition of a new "dewar" SITE2, which describes the IMACS dewar after the
change of chip 6 on August 1, 2005.

adjust-map:
- if the order of a fit is set to a negative number, no correction is made to
that fit.
- diagnostic mode in which fits are plotted.
- fit iterations with exclusion of outlying points

defineobs:
- new parameter added to specify instrument

extract-2dspec:
- wavelength limits default to those defined in map file if set to zero in
parameter file
- option of not subtracting shuffled region in nod&shuffle data
- option of extracting in logarithmic intervals of wavelength
- interactive fitting for displacement of objects along slits

map-spectra:
- option of mapping alignment holes as well as slits
- name of wavelength limits changed in parameter file to conform to those
used by other programs
- fit orders hard-wired into program rather than user selected

process-2spec:
- prompts for bad pixel file used by Sflats and subsky

Sflats:
- wavelength limits default to those defined in map file if set to zero in
parameter file
- uses standard dewar-specific and/or optional user-defined bad pixel map
- cosmic ray rejection eliminated (promised but never implemented in version
1.x)
- option of generated shuffled flats for nod&shuffle data

spectral-lines, spectral-map:
- if line list file is a number, it is treated as a single wavelength line
list
- add option of outputting position of object, or positions of slit ends
rather than slit center

stitch:
- new program to combine LDSS3 files in multi-amplifier readout into one image

subsky:
- wavelength limits default to those defined in map file if set to zero in
parameter file
- add option of 2-dimensional spline fits
- uses standard dewar-specific and/or optional user-defined bad pixel map
- add parameter for ignoring ends of slits

viewspectra:
- additional way to set contrast of spectrum image window
- added button for writing out 1-d spectrum
- options for viewing nod&shuffle data

Several new programs are on the way:
- A program to generate bad pixel files including areas contaminated by zero
and second order grism spectra
- A program to allow spectrophotometric calibration of all slits using
observations of a standard star, either through one aperture or through the
center slit

Bug fixes include:
- error in map-spectra in calculation of slit curvature for slits with
off-center objects
- incorrect handling of ends of slits in subsky
- various minor bug-fixes



Cosmos 1.06 - released 9-1-04
- viewspectra replaces view-1dspec, view-2dspec with enhanced features
- 2-d spectra pipeline scripting program process-2dspec added
- biasflat modified to handle new FITS headers
- cookbook added to documentation
- gains adjusted in biasflat parameter file
- minor bug fixes



Cosmos 1.04 - released 7-15-04
- Well, extract isn't perfectly satisfactory, so an alternate method of
extracting, combining, and CR cleaning multiple spectral frames devised.
- subsky and extract-2dspec modified to output pixel value errors
- extract-2dspec calculates mean offset in object positions to improve
combining frames
- cosmic ray cleaning added to sumspec
- additional features added to view-2dspec
- numerous bugs found in handling of normal (as opposed to nod&shuffle) mode
- programs modified to handle changes to IMACS FITS headers
- miscellaneous minor fixes



Cosmos 1.02 - released 5-1-04
- Sflats modified to better handle bad pixels, columns
- bug fixes



Cosmos 1.00 - released 3-28-04
- extract, the general CR-cleaning, frame combining, and extraction program,
is now installed. It replaces extract-2dspec.
- biasflat changed to pass through more header information
- view-1dspec, 1-d version of view-2dspec added
- bug fixes to programs and installation scripts



Cosmos 0.90 - released 2-8-04
- programs added:
- imcombine8
- display8
- sumspec
- Sflats
- name changed: align-dewar is now called align-mask
- adjust-map now allows one to interpolate between two arc exposures
- slit numbers in map-spectra now start with 1 rather than 0
- tweaks to chip positions in SITE.dewdef
- many small changes and bug fixes