#README
# Skeleton instructions for flattening megacam data 2005.08.02 BAM

#Download and unpack megared.YYYY-MM-DD.tar.gz and calib.YYYY-MM-DD.tar.gz
# The megared file contains the scripts and the calib file contains 
# bad pixel masks and a shutter correction file.

#There is a lot of experimental stuff in this directory right now.
# You can ignore most of it.

# Add the following to your .cshrc 
setenv MEGARED /your/path/Megared

#Add the following to your loginuser.cl:
reset megacam = /your/path/Megared/  # Or whatever the right path is
task $megacam.pkg = megacam$megacam.cl

# Start IRAF
cl

# Copy the subsets file into your directory
# If you have filters other than u,g,r,i,z you may need
# to edit this file to add your filters.  Follow the existing examples.

copy megacam$subsets .

# Load mscred and megacam packages
mscred
megacam

# Initialize the ccdproc parameters (should normally need to be done only)
mscred.instrument=megacam$sao/mmto/mmt/megacam.dat
cl < megacam$ccdproc.par
cl < megacam$flatcombine.par
cl < megacam$megaproc.par

#For data taken before August 2004, repair broken keywords
fixmosaic *.fits fixmos+

# Overscan correct and trim the flats
megaproc overscan+ trim+

# If the flats are less than 1 sec, apply the shutter correction
# Only works for binx2 data
shutcorr corrfil=megacam$shut20050605.fits
# OR for data taken in 36amp mode 
shutcorr corrfil=megacam$shut20050605m.fits

# Combine the flats
flatcombine

# Flatten the data
ccdproc overscan+ trim+ flatcor+ flat="Flat*.fits"

# If the data are < 1 sec, apply the shutter correction (see above)
shutcorr

# Fix bad pixels (must do this after trimming!)
# First add pointers to all the bad pixel files
# These masks are a first stab.  They are appropriate only for binx2 data.
addbpm *.fits bpmaskdir="megacam$Badpix"
# OR for data taken in 36 amp mode  2006-09 and later
addbpm *.fits bpmaskdir="megacam$Badpix_2006_36amp

# Then fix them
ccdproc  fixpix+

# Merge adjacent amplifiers into one fits file.  The merge feature in ccdproc has a bug
# where the merging ends up with a column of blank pixels.  Instead use this script:
# It appends the character 'm' after the filename, so e.g. moo.1234.fits becomes moo.1234m.fits
# This step is not necessary for data taken in 36 amp mode

megamerge *.fits

#---------------------------------------------------------------------
#WCS correction

# See the file megacamwcs.html for more detailed information

Add the following to the front of your path:
$MEGARED $MEGARED/bin
e.g. set path = ($MEGARED $MEGARED/bin $path)

# The WCS written in the image header at the telescope is systematically off by 0.5degrees in rotation.
# Adjust the rotation angle so that the WCS solution works better
cl> fixmosaic *.fits fixmos- fixrot+ fixcen- rotcorr=-0.5

# Install the WCS distortion terms into the image header
cl> zpn *.fits

# Determine the WCS
megawcs -f $MEGARED/M67.0659.outfinal -c tmc -r 0.002 *.fits

# Check that the solution looks good
grep Merit *.outfinal 
# The value should be something like 0.12 (arcsec RMS).  Anything larger than
0.15 should be viewed skeptically.

# SWARP installation
# The out-of-the-box version of swarp does not handle the ZPN wcs properly.
# At CfA, a bug-fixed version of swarp can be found in /home/bmcleod/bin.linux
# Otherwise, download swarp from terapix and patch it.
# This distribution contains patch files for version 2.15,  2.15.6, and 2.15.7
# Here's how I install it:
cd swarp-2.15.7
sh $MEGARED/patchswarp-2.15.7
./configure --prefix=/home/bmcleod --enable-threads
make
make install
# This installs swarp to /home/bmcleod/bin


#
#
#
# Making illumination correction images from SDSS photometry
sdssmatch file.fits
/home/bmcleod/imagesurf/mkillum file.sdss.matched.tab [filter] file.fits Illum.fits
Then normalize it manually.
Divide the data by the Illum.fits file.