Mac Software Hints

The following have been revised to version Ventura (13.5).

Setting up a new Mac or Upgrading to Ventura
Installing IRAF
Installing astrometry.net
Installing Source Extractor
Installing CMFGEN
Installing Michael Mommert's photometry code
Miscellaneous
FIRE
Running Larry's astrometry code
GMOS Mask Design
GMOS reductions (opens in separate window)

Setting up a New Mac or Upgrading to Ventura!

I procrastenated for several years, but I've finally abandoned Mojave 10.14) and with it, 32-bit support for IRAF. It's taken a while for things to become convenient again, but I'm a believer--- come on in, the water's fine! Here's what I've done to make things good for myself; of course, YMMV.

SKIP for M2/M3s...Turn off Syste Integrety Protection (SIP). Starting many O/S versions ago, Apple introduced System Integrity Protection (SIP), which made it more difficult to put directories where you might want them. I'm sure it was well intentioned. They were kind enough to provide a way to turn this off. Note: on my new M2 laptop this step actually wasn't necessary. /usr/local/bin seems to exist, and default locations for a lot of things are /opt. See below.
- Reboot into Pirate mode by holding down the "command" and "r" keys on boot.
- Utilities --> terminal
- csrutil disable
- Reboot back into normal mode.
Do a software update
However...you probably want to do system settings-->security-->Full Disk Access-->Terminal on. How else are you going to have fun?
Set up vpn access if this is a laptop. At lowell, this has gotten pretty insane. See https://confluence.lowell.edu/display/PUB/VPN.
Go to the app store and download the latest XCODE. Once it's installed, do a xcode-select --install. At some point it will ask you to accept the license agreement. If this hasn't popped up to the front, eventually you'll have trouble, so look around for it.
Associate MAC address with name [This is a local Lowell thing]
Settings->General-->Show scroll bars "always". Jeez. (Is this still a thing? Check! Answer: sadly, yes)
Install or update XQUARTZ: https://www.xquartz.org
Change the default shell to tcsh. Obviously this is a personal choice, but I don't like bash. (Why? Because I learned csh when I came to Unix from VMS.) To do this go to sys pref--->accounts; do a CNTL-click on the name (after unlocking) and change the login shell to tcsh. Copy over a working .tcshrc from somewhere.
Change some things. Again, some of these are personal preferences but not the emulate three button one.
- system preferecnes--->sharing--->turn on screen sharing, file sharing, remote login; put in the name
- system preferences--->trackpad-->scrool and zoom--->scroll direction: natural UNcheck
- Sys pref-->mouse-->primary (left), buttone 3 middle, secondary right
- x11-->preferences--->input--Emululate three button mouse
- sudo chflags norestricted /usr/local
- sudo mkdir /usr/local/bin; sudo chown yourself /usr/local/bin
- If you're going to ever compile the cmfgen version of pgplot, find a version of stdint.h and put it in /usr/include. Here is a copy Not clear if this is still relevant--check!
- Fix ssh: Not clear if this is still relevant either. Check!
  - cd /private/etc/ssh
  - sudo vi ssh_config
  - ForwardAgent yes
  - ForwardX11 yes
  - sudo vi sshd_config
  - X11Forwarding yes
- SKIP IF YOU NEVER TURNED IT OFF. If you want SIP back on, go back into recovery mode, and do a "csrutil enable."
Install ds9
Install homebrew: see https://brew.sh/
Install source-extractor: "brew install sextractor"
Install Super Mongo
- If you have a site license (Lowell does) you can obtain a copy that "makes" on a Mac by going to https://www.astro.princeton.edu/~rhl/sm/distribution/sm-latest.tar.gz. You'll need their login and site password. Try emailing Patricia Monger
Install TeXShop and TeX. Yes, I know a lot of the kids these days are using overleaf. But not the **cool** kids. If you're simply updating, ignore the next thing and just update TeXShop.
- Go to the TeXShop Downloads page. You need more than TexShop; you'll need the whole kit-and-kaboodle at http://www.tug.org/mactex/
If you want to do the whole aasTeX thing and have LaTeX find them no matter where you are....
- mkdir ~/Library/texmf
- mkdir ~/Library/texmf/tex
- mkdir ~/Library/texmf/tex/latex
- mkdir ~/Library/texmf/bibtex
- mkdir ~/Library/texmf/bibtex/bst
- mkdir ~/Library/texmf/bibtex/bib
- Download aastex52 package and stick in the latex subdirectory above
- Download apj.bst and stick it in the bst subdirectory
- Create your own masterbib.bib and stick it in the bib subdirectory
Do some brewing:
- Install homebrew: see https://docs.brew.sh/Installation
- brew install (or upgrade) gfortran
- brew install (or upgrade) inetutils
- brew install (or upgrade) sextractor
- brew install astrometry-net (more on this below).
Now fix the path issues: /opt/homebrew/bin/brew bundle dump and add /opt/homebrew/bin to your path.
To keep astrometry-net happy, you'll need to do a ln -s sex source-extractor in the bin directory.
Install IRAF

Installing IRAF

As of January 7, 2024 this has gotten a whole better!

Go to https:/iraf.noirlab.edu and download the macOS .dmg file.
Move the four apps into the application folder shown on the image.
Click on "iraf.app" in the applications folder. It will try to open itself and xgterm. You will have to fight with OSX security to get permission for this by going to system settings-->"privacy and security" and scrolling to near the bottom, and you'll have to do this at least twice, once for iraf and once for xgterm, but keep at it.
In theory, this should have entered a "source .iraf/setup.csh" command into your .tcshrc (if using tsch) or .iraf/setup.sh into your profile (or whatever ash uses have). This week it wasn't, so I explictly added it.
If you want to make your xgterm look like mine, edit .iraf/initrc so that bg_color=lightskyblue1, fg_color=gray30; nrows=30, and font_name=9x15Bold.
Move .iraf/loginuser.cl up a level to your home directory, and insert a reset use_new_imt=no. Add any task definitions you need.

Installing the Astrometry.net software

The astrometry.net software is pretty neat! You run it, and it blindly finds the wcs for a frame, if you're lucky. So far, in 3 out of 3 frames (one from the Lowell 31-inch, one from the 4.3-meter DCT and LMI, and one from the Swope of a very croweded field in the LMC) it's worked beautifully.

Things have gotten a lot easier to install. I found once I brought up Homebrew, I could install with only minimal head-bashing:

Download and install Homebrew as above: https://docs.brew.sh/Installation
Okay, hold on. On Apple Silicon machines (M1, M2) brew winds up in /opt/Homebrew/bin/brew. This is fine, but guess what--when you brew things they no longer have a link added to /usr/local/bin. Instead, they exist in their own little world, like /opt/homebrew/Cellar/astrometry-net/0.94_3/bin/solve-field. Nothing inconvenient about THAT. But there is a solution. When you're done with brewing a bunch of stuff, do a /opt/Homebrew/bin/brew bundle dump. This at least puts links in /opt/Homebrew/bin. So, you can add THAT to your path.
brew install astrometry-net
Install the indicies.
- Download the 2MASS indicies, the TYCHO indicies and the USNO-B1.0indicies and stick them somewhere where you have a spare 65Gb of space.
- Edit the /usr/local/Cellar/astrometry-net/etc/astrometry.cfg file to reflect where you've put the indicies, i.e., something like this:
```
# In which directories should we search for indices?
add_path /Volumes/pepe/astromindicies/2MASS-indicies
add_path /Volumes/pepe/astromindicies/TYCHO-indicies
add_path /Volumes/pepe/astromindicies/USNO-indicies 
```
Add /usr/local/astrometry/bin to your path
Try it on a
test image:
- solve-field --overwrite --scale-units arcsecperpix --scale-low 0.44 --scale-high 0.46 --ra 23.33 --dec 29.27 --radius 0.5 121028-987.fits
- solve-field --overwrite --scale-units arcsecperpix --scale-low 0.43 --scale-high 0.44 --ra 84.0 --dec -69.2 --radius 0.5 n2044test.fits
- solve-field --overwrite --scale-units arcsecperpix --scale-low 0.23 --scale-high 0.25 --ra 179.8 --dec 12.3 --radius 0.1 lmi.0079.fits
- solve-field --overwrite --scale-units arcsecperpix --scale-low 0.43 --scale-high 0.44 --ra 92.08 --dec -71.96 --radius 0.3 --tweak-order 1 --no-plots --use-sextractor -N LMC000iCIIt1.fits LMC000iCII.fits
- Can add:
  - --use-sextractor (newer versions: --use-source-extrator)
  - --no-tweak or --tweak-order 1
  - --no-remove-lines (very useful when it won't solve). Should probably be the default.

Source Extractor

brew install sextrator

CMFGEN

CMFGEN is John Hillier's wonderful radiative transfer code for hot stars with stellar winds. The care and feeding of the code is beyond the scope of the current notes. Hese are some hints that should help in getting in getting the code up and running.

In the olden days, it was best to use the PGF95 compiler on a Mac. However, NVIDA bought out the Portland Group and they no longer support Macs, and the latest (final) version of PGF95 nominally won't work on any O/S later than Mojave. So, I have revised the instructions here for getting it going on my new M2 (Apple Silicon) Macbook Air. I've retained the PGF95 instructions below as I'm still maintaining a machine or two with these.

Ventura and Apple M2 (works on Intel as well)

Download the CMFGEN source code and the Atomic files from https://sites.pitt.edu/~hillier/web/CMFGEN.htm.
I like to organize things as follows as this allows me to maintain (and switch) to older versions.
- mv cur_cmf cur_cmf28jun23
- mv atomic atomic26jun23
- ln -s cur_cmf28jun23 cur_cmf
- ln -s atomic26jun23 atomic
Make sure you have XCODE and the the command line tools installed. (Use " xcode-select --install" after downloading XCODE and make sure you accept the license agreement. This usually requires a bit of fiddling.)
Download the latest version of gfortran. I do this using homebrew; see instructions elsewhere in this document.
Now for the trickiest part: compiling pgplot!

Compiling pgplot

Download the official version of PGPLOT from the Caltech website: ftp://ftp.astro.caltech.edu/pub/pgplot/pgplot5.2.tar.gz. I found that my browser no longer accepts ftp addresss so cough, cough .
So, the directory structure matters. I use a somewhat convoluted structure:
- mkdir pgplotm1
- mkdir pgplotm1/pgplot
- mkdir pgplotm1/pgplot/pgplot
- tar -xvf pgplot522.tar [creates a subdirectory pgplot]
- mv pgplotscr (from the tar file) to pgplotm1/pgplot.
- At this point all the stuff is in pgplotm1/pgplot/pgplotsrc, and pgplotm1/pgplot/pgplot is empty. That will change when we compile.
I have never had any luck with their instructions to make a make file. John was kind enough to provide me with a Makefile that worked for him. I've alternated it slightly as XCODE does change where the libraries are kept. Here is a copy Makefile. You'll have to change the directory names.
Stick the make file in the pgplotm1/pgplot/pgplot directory, and NOT in the pgplotm1/pgplot/pgplotsrc file.
cp pgplotm1/pgplot/pgplotsrc/drivers.list pgplotm1/pgplot/pgplot/. Uncomment out the NUDRIV, the two XWDRIV entries, the 2 PNDRIV, and the 4 PSDRIV entries.
Do a make clean followed by a make all. Hopefully that will all work! At this point, you should have a libpgplot.a and a pgxwin_server in your pgplotm1/pgplot/pgplot directory. Those are what you need! If not, keep fiddling.

Back to compiling cmfgen

There is only one file we have to change before we compile:

You need to modify cur_cmf/Makefile_definitions. Here's what we've used successfully with the gfortran compiler: Makefile_definitions You'll need to modified the INSTALL_DIR definition and the PGLIB definitions, the latter to show where libpgplot.a is. (For instance, -L/Users/massey/pgplotm1/pgplot/pgplot/ -lpgplot).

Well, that should do it. Do a make clean follwed by a make all. Don't worry about minor warning messages.

A few more things to do:

Edit cur_cmf/com/aliases_for_cmfgen.sh to show where cur_cmf and atomic are locted.
Put the following in your .tcshrc:
- source /Volumes/strax/cmfgen/cur_cmf/com/aliases_for_cmfgen.sh
- setenv PGPLOT_DEV /xserve
- setenv PGPLOT_FONT /users/massey/pgplotm1/pgplot/pgplot/grfont.dat setenv NCPUS 4 limit stacksize unlimited
When you go to plot a spectrum make sure that you have the /pgplotm1/pgplot/pgplot/pgxwin_server running.

Old Instructions for compiling cmfgen with PGF95 and Mojave

You will seriously need to buy the PGF95 compiler.
- Hints in getting the damn license server to work:
  - You **may** be able to just get by doing a "lmreread"
  - In getting the permanet license, first do a "lmutil lmhostid" to see which MAC address the damn thing is picking up.
  - Starting up the license daemon:
    - sudo bash
    - cd /opt/bin/osx86-64/2018/bin
    - sudo cp com.pgroup.flexlm.plist /Library/LaunchDaemons
    - sudo chown root:wheel /Library/LaunchDaemons/com.pgroup.flexlm.plist
    - sudo chmod 0644 /Library/LaunchDaemons/com.pgroup.flexlm.plist
    - sudo launchctl load /Library/LaunchDaemons/com.pgroup.flexlm.plist.
    - When that fails, just do a /opt/pgi/osx86-64/18.3/bin/lmgrd
    - Recently I've been trying this and getting a message about not being able to open a port. Turns out that here was some conflict with the idl83 lmgrd. Do a ps -ax | grep lmgrd. Now...if you just kill it, it will restart. So, I did something more draconian and did a mv of the executible in the IDL directory to lmgrdold. I then rebooted. At that point the 2018 PGI version came to life, and it read my license file fine and I could compile again. Lord knows what's going to happen when I go to run IDL though...
  - Strongly recommend downloading latest xcode and trying to open it (so that you install the other stuff) before doing much else.
  - For the pgfortran compiler to work, you need to do a sudo ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/crt1.o /usr/lib/crt1.o
  - For Yosemite you will also need a
    - sudo ln -s /opt/X11 /usr/X11R6
    - sudo ln -s /opt/X11 /usr/X11
  - For El Capitan/Sierra, one needs to find an older version of stdint.h and put it in /usr/include. Here is a copy This is needed for compiling pgplot.
- In the .tcshrc put
  - setenv PGI /opt/pgi
  - setenv LM_LICENSE_FILE $PGI/license.dat
  - source /Volumes/strax/cmfgen/cur_cmf/com/aliases_for_cmfgen.sh
  - set path = ($PGI/osx8-64/15.3/bin/ $path)
  - setenv PGPLOT_DEV /xserve
  - setenv PGPLOT_DIR /Volumes/strax/pgplotorig/pgplot/pgplot (pretty sure this line does NOTHING)
  - setenv PGPLOT_FONT /Volumes/strax/pgplotorig/pgplot/pgplot/grfont.dat
  - setenv NCPUS 4
  - limit stacksize unlimited
One needs the "special" Mac version of pgplot. Here it is. cd to pgplot/pgplot (not pgplotsrc!), "fix" the directory names at the top in Makefile, and then do a "make clean" and a "make all". It will bomb with an error message when it tries to create the cpgdemo stuff (Undefined symbols in MAIN) but you will find to your surprise that libpgplot.a has been created! Joy!
Download the CMFGEN source files from the above link. Create a subdirectory cur_cmf_date and stick the stuff there. Create a symbolic link ln -s cur_cmf_date cur_cmf.
Download the latest and great atomic data as well from the above link.
Edit cmfgen/cur_cmf/Makefile_definitions so it looks something like this.
If you update the version of the compiler, make sure you change the library location in the Makefile_definitions.
NO LONGER NEEDED: Modify the Makefile definitions in "subs" and "plane" to invoke FZ rather than whatever flag it users. This gets around a bug with 14.10 that affects subs/fg_j_cmf_v9.f and plane/fg_j_cmf_v12.f.
edit cur_cmf/com/aliases_for_cmfgen.sh to contain the right paths
make clean
make all
So, you think you're all set, don't you? Well, you're not. You're going to have so start the server: /Volumes/strax/PGPLOTOrig/pgplot11.0/pgplot/pgxwin_server &
While how to use CMFGEN is way beyond the scope of this little note, Kathryn's CMFGENGuide is invaluable.

Michael's photometry routines (Thanks to NickM)

This section is now outdated.

Install homebrew:
- bash
- ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
- brew doctor
Install anaconda3:
- https://www.anaconda.com/distribution/
- conda update conda
- conda config --add channels http://ssb.stsci.edu/astroconda
- conda install iraf-all pyraf-all stsci
- add to .bash_profile: source activate base
- Add to .condarc file in home directory: changeps1: False
- conda install -c astropy pyephem astroquery
- conda install -c conda-forge uncertainties lmfit pysftp scikit-image cfitsio
- conda install -c anaconda future pillow
Update pip:
- pip install --upgrade pip
Install sextractor and scamp:
- brew install brewsci/science/sextractor
- brew install brewsci/science/scamp
Install extra software:
- brew install wget
- brew install imagemagick
- brew install GraphicsMagick
- brew install inetutils
git clone https://github.com/mommermi/photometrypipeline
Add to .bashrc:
- export PHOTPIPEDIR=/Users/massey/photometrypipeline
- export PATH=/Users/massey/photometrypipeline:$PATH

Miscellanous

Dealing with lo-gateway:
- To ssh or sftp TO lo-gateway use sftp -oHostKeyAlgorithms=+ssh-rsa lo-gateway
- To ssh, sftp, scp, or rsync FROM lo-gateway, use -oHostKeyAlorithms= ecdsa-sha2-nistp256
- Yes, you CAN put this in your .ssh/config file. My config file on lo-gateway now says: Hosts * and then on an indented line: HostKeyAlgorithms ecdsa-sha2-nistp256
quarantined tag "@" in an ls -l ? Do a xattr -d com.apple.quarantine filename. If that doesn't work, try a "-c" instead of a -d
A very useful trick to see what's being loaded in python
- DYLD_PRINT_LIBRARIES=1 pyraf [say]
With XCode 10 the "include" folder is gone so gcc doesn't work. You need to do an "open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg"
awk '{print substr($1,1,13)}' filename > somethingelse Will print the first 13 characters of the first field.
awk '{print $4 " " $46 " " $47 }' test.tab > RBC.txt will print the 4th, 46th, and 47th word with spaces in between them!
Set up public/private key to eliminate need for password:
- On the local machine do a ssh-keygen. Hit a CR for the passphrase
- Copy the key to the remote machine: ssh-copy-id -i /users/massey/.ssh/id_rsa observer@dct-obs1 [enter password]
- Test by doing an ssh observer@dct-obs1. Hopefully you won't have to enter the password every again.
To set up a cron job for a remote backup:
- Go to the disk you want to copy to, say /volumes/Gandalf
- Create a file "rsync_script" that looks like this:
  - #!/bin/sh
  - rsync -avz observer@dct-obs1:/lmi/2017* /volumes/Gandalf/.
- Now create the cron job:
  - crontab -e
  - Insert: 30 13 * * * /Volumes/Gandalf/rsync_script
  - The stuff at the beginning is Min (0-59), Hour (0-23), Day of month (1-31), Month (1-12), Day of Week (0-7).
- Should be good to go! If it doesn't work, try a "set nonomatch"
rsync -avP obs1@llama.lco.cl:/VOLUMES/DATA_BAADE/MAGE/ut221001_02 .
cp -av preserves links
Terminal line profiler: /usr/sbin/system_profiler SPHardwareDataType
Which version of XCODE: /Developer/usr/bin/xcodebuild -version
open -a "Dropbox.app"
In compiling John Thorstensen old skycalc.c code under Mojave, it complained it couldn't find stdio.h. I already had command-line-tools installed, but I needed to do a open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg. Once I did that, a gcc skycalc.c -o skycalc -Im worked with a few warning messages.

FIRE

Rob Simcoe (MIT) provides some excellent reduction software for his amazing Magellan instrument FIRE. I did find some of the installation and usage instructions a bit confusing. The following instructions were constructed with some help from Jane Rigby.

To access the manual one needs an account on the Wiki. Follow the instructions on how to get an account, and then email Rob as instructed. One delay was due to the fact that he can't actually add you until you've tried unsuccessfully to log in once.
Download the relevant software: This is revised Jan 1, 2021
- mkdir idlstuff
- cd idlstuff
- svn co https://svn.sdss.org/public/repo/sdss/idlutils/trunk/ idlutils
- svn co https://svn.sdss.org/public/repo/eboss/idlspec2d/ idlspec2d
- cd idlspec2d ; mv trunk/* . ; cd ..
- git clone https://github.com/profxj/xidl.git
- svn export svn://pele.mit.edu//FIRE FIREHOSE
- svn export svn://pele.mit.edu/firehose_test Test
Define numerous environmental variables:
- setenv IDL_LOCAL /users/massey/idlstuff
- setenv IDL_DIR /Applications/exelis/idl
- setenv IDLUTILS_DIR $IDL_LOCAL/idlutils
- setenv XIDL_DIR $IDL_LOCAL/xidl
- setenv IDLSPEC2D_DIR $IDL_LOCAL/idlspec2d
- setenv FIRE_DIR $IDL_LOCAL/FIREHOSE/
- setenv IDL_PATH +/users/massey/idlstuff/FIREHOSE:+/users/massey/idlstuff/idlspec2d:+/users/massey/idlstuff/idlutils/goddard/pro:+/users/massey/idlstuff/idlutils/pro:+/users/massey/idlstuff/xidl:+/Applications/exelis/idl/lib:
- set path=($path /users/massey/idlstuff/idlutils/bin)
Compile the software using "evilmake":
- cd $IDLUTILS_DIR
- evilmake clean
- evilmake all
- cd $IDLSPEC2D_DIR
- evilmake clean
- evilmake all
- cd $XIDL_DIR
- evilmake clean
- evilmake all
Okay, there's a new problem with Quartz 2.7.11. You need to do the following or else you'll get a scary error message: Error: attempt to add non-widget child "dsm" to parent "idl" which supports only widgets
- sudo mv /opt/X11/lib/libXt.6.dylib{,.bak}
- sudo cp /opt/X11/lib{/flat_namespace,}/libXt.6.dylib
Here's another fun fact: if some of your files have a * after them, do a ls -l. If you see a "@" it means they have an "attribute." This really screws up the pipeline. Get rid of those by doing a attr -c *.fits
It also hates files that are +x. Do a chmod a-x *.fits
Take the software for a test drive:
cd $IDL_LOCAL/Test/redux
NOTE: When you're doing this with your own data, you need to have created both a Raw and a Redux subdirectory. Be sure you're in the Redux subdirectory when you start up idl.
idl
firehose
- Setup tab
  - Raw Directory: set to default and check that it shows the right path.
  - Redux Director: set to default and check that it should the righ path.
  - Observing catalog: Browse your way over to it.
- Trace tab
  - Select one or multiple QF flats and hit "trace orders." (NOTE: I always get an error if I select multiple flats. It's supposed to work. Seems to be fixed Jan 2021.) A plot similar to this will be displayed:
  - The xatv window will pop up showing the orders outlined:
- Flats tab
  - Select all of the QFs for the flat field images (1-10 for the test data; image 11 is incorrectly labeled). If you are combining flats from more than one night, check to see if there are shifts. You might need to put them in a separate directory so you can choose them all, and revise the setup temporarily.
  - Select the sky flats for the illum flats (15+16 for the test data). NOTE: Make sure your sky flats have EXPTYPE set to "TrcFlat"
  - Select an arc for the slit tilt. I know the manual says to just use a long exposure, but when I did this I had nothing but trouble. The arcs worked wonderfully.
  - Select the orders mask you just created for the Orders Mask.
  - Hit Make Flat Field. Go out for coffee.
  - Viewer pops up, flat field w orders traced out, Hit Done.
  - Some illumination function plots pop up.
  - Viewer pops up with flatfield. Hit Done.
- Structure tab
  - Flats tab should be populated thanks to the previous step.
  - Generate structure. Give it a few seconds.
  - Edit (and Save) Structure. Make things are right. If not, fix.
  - For the test data: the title of fire_0011.fits is "QF" but it's actually an arc. Even more confusing is that it is an arc that crashes the program in the next step. Change its type to "unknown."
  - Hit Done.
  - NOTE: I you need to redo some subsequent steps you can do a "Load Structure"
- Extract tab
  - Highlight the object(s) you want.
  - You can do this the easy way or the hard way....
    - Easy way: In Preferences, keep the Object/Aperture Finding automated and hit "Run Pipeline." Don't use the boxcar; use the full blown.
    - Hard way: In Preferences, set the Object/Aperture to Interactive/User Fits.The following is parapharased from Jane Rigby:
      Read the manual carefully to learn how to best extract your targets. Generally there are three cases: (a) Very strong continuum source, which allows you to (in principle) use a boxcar extraction. This runs fast, but produces inferior sky subtraction. (b) Fairly strong continuum source. This is great, as the GUI will do most of the work for you. All you have to do, when the viewer pops up, is find the continuum ridge line in any order, mouse over it, hit space bar, hit O (capital oh), and then hit Done. The GUI will find the trace. (c) Objects with strong emission lines but weak to non-existent continuum. This is the hardest case, but there is a specific options who allows one to fit the spatial profile from a bright emission line, and then use optimal extraction using that profile, adopting the trace from of the telluric star. [Phil: to me, this sounds similar to IRAF's aperture extraction using another star as the reference. I'm surprised that it doesn't just adopt the profile from the standard as well.] Here's how to deal with "c."
      - Identify a bright emission line when the view pops up.
      - Change MouseMode to Zoom, and click the line to zoom in on it.
      - The panner box at upper right works like ds9’s, if that’s more comfortable.
        
        Put the cursor just below the emission line and hit "B." Then put the cursor right above the emission line and hit "T."
        A gui comes up and fits a bspline:
        
        Note that there's a help menu at top of gui.
        You can change the fitting function via the gui.
        Delete points w "D". Add data pts w left click (to set zero at left).
        "R" plots residuals, "V" plots values.
        "u" increases order of fit, "d” decreases.
        Hit Done when satisfied. Then it does the sky sub w/o fitting the profile. There is no gui feedback yet on this part.
- Telluric Correction Tab
  - The telluric correction relies upon "Xtellcor" and associated routines from the Spextool package. A complete version of the manual (written by Michael Cushing, William Vacca, and John Rayner) can be found here; see Chapter 6. I found that the instructions at the APO TripleSpecTool were a bit easier to follow; see Section 10.2. In truth, the on-line help window is quite good too.
    Still, it took me about a day to figure out how the damn cursor works. You know how Doug Tody eventually implemented cursor readback in IRAF about 30 years ago? In the subsequent decades many of us got used to the idea that if the instructions tell you to hit an "n," you put the cursor where you want and hit an "n" and the software reads the x and y position as well as the "n" and acts accordingly. This is not the philosophy of Spextool, apparently. Instead, what the manual actually means is that you hit an "n" and that after that you left-click the mouse at the position you want, and that you are simply in "n" mode until you hit another key, or make a mistake. It takes a bit of getting used to, but so did the transition from thumbwheels on Tektronix 4010. Sigh.
    So, here's what I did.
    - Expand the folder(s) for the "targets to calibrate tellurics." Click on the first one in the tree.
    - Correct Tellurics. A little "fire_telluric" window should pop up allowing you to select the telluric standard obervations relevant to this exposure. Select them and then click "continue." I don't know what it would do if there were two different stars.
    - A very large plot will pop up (in "x_splot") showing you all of the orders. Presumably this is so you can identify the fact that Order 26 around 1.00 micron contains the strong Pa Delta line (n=7 to 3) at 1.005 microns. Got it. Hit "q."
    - The fire_xtellcor window will pop up identifying the telluric observations for this target. It should be populated with the file names of the telluric (standard) star observations, the magnitudes of the telluric standard, and the name of the object spectrum. If the magnitudes aren't there, look them up and enter them.
    - The main thing that is to come up with a proper convolution kernal between the A0V star telluric observation you made and some standard Vega model. In box 2 make sure the radio button for "Deconvolution" is selected, and that Order 26 is selected, as this is what contains the Pa Delta line.
    - BEFORE YOU DO ANYTHING ELSE, HIT THE "Help" button on the bottom of the gui because this will become grayed out once you actually need it. (Doesn't anyone screen these calls?)
    - Hit "Construct Kernel."
    - You will be confronted wih what is apparently a simplified version of the Xconkern Spextools window. You'll see the spectrum of the telluric standard in white exending from about 0.972 to 1.034 microns with the big whopping Pa Delta line pretty much in the middle.
    - Click on "n" to inform the software that you are planning to mark the continuum regions in order to fit the continuum. It's a good question how close to the line you should mark. The example shown in the APO guide is silly; don't do that! I did okay by marking 0.973 to about 0.996 on the left side and 1.016 to 1.034 on the right and using an 11th order. Recently I've been using "n" to define two regions on the left and two on the right. The normalization matters a lot!
    - Now you have to click "Normalized spectrum" and select the wavelength region that contains "just" the line. You might find it useful to use the zoom feature: hit "z" and then click twice with the left-mouse to outline the regions you want. Or you can try "x". w will unzoom.
    - You must now "select" using the s key: hit s, and then mark the left and the right side of the spectral line using left-clicks on the mouse.
    - Now hit "Construct kernel." The holy grail here (according to the APO guide) is maximum deviations less than 1.5% ad an RM deviation less than 0.7%. Using the sample data I could not come close to achieving this. I did manage to achieve errors that were about twice that. If you don't get anything you like, go back and redo the normalization. Hit "accept."
    - Okay, we're back to thefire_xtellcor. Hit Scale lines. You'll be happier with just hitting "accept." If the spectrum is missing, you neglected to add the B and V magnitudes if they were missing. Mess around with "e" and dragging points with all of the orders until you're happy. Hit "accept." My experience is that this is too obscure to mess wit
    - Decide what units you want (such as ers/sec/cm^2/A) and hit "construct telluric spectra"
    - Determine Shift. So, this turns out to matter: Select Aperture 01 and Order 28. Do an "s" and then click on the left and then the right of that region with a whole bunch of telluric stuff. Hit find auto. Don't be surprised to get a value like -1.50. Hit accept, and then Apply to All orders.
    - Write File.
    - Repeat for the other 3 program (or 7) program images. Each time select all 4 of the telluric observations. The nice thing is that a much smaller window will pop up. You can just hit "Load Spectra", "Apply to All orders," and "Correct spectrum."
    - Do a Combine. Make sure it was the correct number (4 or 8, usually).

Running Larry's astrometry code

The Buie/Wasserman IDL package produces excellent results on LMI images, but the naming conventions are idiocentric.

Use apphot's "center" or psf fitting to produce a file of accurate x and y positions.
Hack on m31makeobj.f So it produces:
- fort.9 which contains an imcopy of the image to a date-based image name.
- a "Mask*.obj" file that contains some magic numbers and a list of 0-indexed x and ys.
Run m31makeobj
cl < fort.9
copy lmi.key one level above your working directory
copy astrom.inf into your working directory
copy dofind.pro to your working directory and edit:
- Update the root name
- Update the directory name to your working directory ending with a "/"
- idl
- dofind,1,5 if you have rootname.001, .002, .003. If it doesn't work you probably have screwed up the directory name.
- mkdir SRC and mv *.src SRC
- edit doast.pro to include the right root name and directory name.
- doast,1,5
- Results are in *.ast. Other fun files:
  - fitcoeff.dat
  - Refstars/image
  - centers.dat

GMOS Software

Designing a slitlet mask

Download a DDS image. Example m33.fits[0]
Mess with ds9 and region files deciding that where it makes sense to put masks, and approximately angle. Keep in mind parallactic angles.
Make list of objects and potential alignment stars (MosA.in) including priorities.
When you're close, make a smaller version of the dss image, i.e., dssE.fits[0].
Bring up the gemini IRAF. Two ways currently:
1. Ureka
  - ur_setup
  - cl
2. anacoda [installation instructions below]
  - bash
  - source .bash_profile
  - conda activate iraf27a
  - cd iraf
  - cl
gmskcreate
Note: the naming convention is stupidly important. "GMI" images are what gets used by GMMPS.
- indata="MosA19.in"
- gprgid="GN-2020B-Q-237"
- instrument="gmos-n"
- rafield=1.55138888889 [can enter as HH:MM:SS.SSS]
- decfield=30.527777778 [can enter as +DD:MM:SS.SS]
- pa=340
- fl_getim=yes
- inimage="dssA.fits[0]"
- outimage="GN2020BQ237-01"
- fl_getxy=yes
- outcoords="GN2020BQ237-01.coo" (not used by anything)
- outtab="GMIGN2018BQ228-01_OT.fits"
- iraunits="hours"
- fraunits="hours"
- slitszx=1
- slitszy=5
- verbose=yes
gmmps: Make sure you have the latest version (in 2020 I used 1.5.2). I could not compile the code, so I used the binary versions.
gmmps
- File-->open-->GMIGN2020B237-01.fits
- GMMPS-->Load Object Table-->GMIGN2020BQ237-01_OT.fits
- Do any editing. For instance, I got rid of 501 and 599 and 598 was supposed to be better.
- Configure mask
- Pick grating, no filter, and reasonable CWL
- No to pack spectra
- min sep 4 pixels
- wiggle 15%
- Make mask (or whatever). See if everyone got on.
- Now go through and try to make the slits longer by changing 5-->10. Update slit. After each change do a new Make mask.
- Note: GMMPS isn't good at counting. The number of 0/1/2/3
- GMMPS Load ODF. Check that 4686 is clear. Make sure that everything looks groovy.
- Rename the out GMIGN2020BQ237-01_OTODF1.fits files to GN2020BQ237-01_ODF.fits without the GMI at the start, or th OT in the middle or the 1 at the end.
- Don't try to load a .gz file. You can, but as soon as you go to load an OT or ODF very bad things happen.