Fine-tuning (K)ubuntu and installing some astro/math packages

Ubuntu, is one of the best linux distros currently (as of 2009 Feb 11). However the live CD that you can download from the Ubuntu website is pretty minimalistic. Most likely you will need to install additional libraries/software. There are many, many webpages devoted to setting up your desktop so that it looks pretty, flashy and play all kinds of media. As as astronomer/astrophysicist, I have a few additional requirements, viz. installing the astronomical software (e.g. HEASOFT, ISIS, IRAF), mathematics libraries (e.g. GSL), and plotting packages (e.g. gnuplot and pgplot). Some of these (and their pre-requisites) are non-trivial and takes a fair amount of searching the internet. Therefore I am trying to put these things together here, so it can be helpful (mainly to me, but maybe others too) for future reference.

Disclaimer: These settings are what I like (today) … so beware …

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0. Random, unorganized notes

2009 Jun 19: The KDE software updater marks the linux kernel upgrades as 'blocked' and wouldn't install them by default. The way to force the kernel upgrade seems to be via 'sudo aptitude full-upgrade'.

1. Setting up Kubuntu

1.1 Connect to the internet and run a full system update/upgrade (click to show)

sudo aptitude update

1.2 Go from Ubuntu to Kubuntu (if you downloaded the Ubuntu CD). Also I can't live without vi. (click to show)

sudo aptitude install vim-gnome vim vim-gtk kubuntu-desktop && \
 sudo aptitude update

1.3 Install medibuntu repository (click to show)

sudo wget --output-document=/etc/apt/sources.list.d/medibuntu.list http://www.medibuntu.org/sources.list.d/$(lsb_release -cs).list && sudo apt-get --quiet update && sudo apt-get --yes --quiet --allow-unauthenticated install medibuntu-keyring && sudo apt-get --quiet update

sudo apt-get --yes install app-install-data-medibuntu apport-hooks-medibuntu

1.4 Some additional packages, libraries that I will need (click to show)

sudo aptitude install libgd2-xpm-dev gfortran g++  \
 libncurses5-dev x-dev libx11-dev libxt-dev libreadline5-dev  \
 gv stellarium autopano-sift enblend hugin libdvdcss2 eog lynx    \
 w32codecs vlc mencoder mplayer mplayer-fonts mplayer-skins   \
 startupmanager grub-splashimages kubuntu-grub-splashimages   \
 gramps gimp doxygen kolourpaint4 vim-gnome vim vim-gtk enscript ncftp \
 skype acroread acroread-plugins and mozilla-acroread tree      \
 mozilla-mplayer gtk2-engines-qtcurve firestarter libgsl0-dev \
 nedit gparted csh tcsh mailutils openssh-server subversion \
 texlive texmaker kile manpages-dev valgrind povray gwenview tofrodos \
 kaffeine gtk-recordmydesktop 
sudo aptitude clean

Maybe good to reboot at this point and make sure everything is working properly.

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2. Then a few more (optional) fine-tunings that I like (and most others don't)

2.1 Start->System Settings->Notifications->Turn of all sounds.

2.2 Start->System Settings->Window Behavior->Under 'Focus' tab, in Focus box, change 'Policy' to 'Focus follows mouse', check 'Auto Raise' with Delay 500ms. Also make the titlebar expands vertically on double click.

2.3 I hate KDE wallet. Disable it: xterm->kwalletmanager->configure kwallet

2.4 Add logoff/shutdown applet to panel.

2.5 Configure the clock in the panel to show day of the week, and also the seconds. I like when the clock has the same fonts as the rest (Sans Serif 9).

2.6 To solve the problem with check-boxes on Firefox (hope they fix it quickly): Start -> System settings -> Appearance -> GTK Styles and Fonts -> Use another style -> QtCurve

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3. Now to the non-standard mathematics/astronomy/astrophysics packages

Note: The version numbers change quite rapidly for these software. These commands assume whatever is the most recent version now (2009 Feb 11). Therefore you may need to edit the commands accordingly. Also, I like to install these in the directory ~/installed/software-name-<version>. Also the sequence of installation is slightly important; particularly you may want to install ISIS after heasoft if you want to link ISIS to heasoft and thus be able to install the XSPEC models.

Update 2009 Sep 25: Maybe I was slow to learn this, but you no longer need to install Pgplot and cfitsio yourself before installing ISIS as long as you have installed heasoft beforehand. You only need to install s-lang. Also VERY, VERY important … use the same set of compilers for compiling s-lang/heasoft/ISIS and preferably the other ISIS modules/accessories like slirp, slgsl etc.

3.1 Install gsl (click to show)

Not needed if you already have it installed, e.g. via the long 'sudo aptitude install …' above. Otherwise

sudo aptitude install libgsl0-dev

To install from source

wget ftp://ftp.gnu.org/gnu/gsl/gsl-1.13.tar.gz
tar -zxf gsl-1.13.tar.gz 
cd gsl-1.13
mkdir -p /usr/Gemini1/dmaitra/installed/gsl-1.13
./configure --prefix=/usr/Gemini1/dmaitra/installed/gsl-1.13
make
make check > log 2>&1 # All tests passed
make install
cd ../
rm -rf gsl-1.13*

3.2 Install gnuplot (click to show)

Download .tar.gz from sourceforge.
Then following the instructions from http://www.miscdebris.net/blog/2007/04/27/install-gnuplot-on-ubuntu/

# Unless libgd2-xpm-dev is already installed e.g. via the 
# long 'sudo aptitude install ... command'
sudo aptitude install libgd2-xpm-dev

# Download and install PDFlib Lite
cd ~/src/
wget http://www.pdflib.com/binaries/PDFlib/703/PDFlib-Lite-7.0.3.tar.gz
tar xzf PDFlib-Lite-7.0.3.tar.gz
cd PDFlib-Lite-7.0.3
./configure
make
sudo make install
sudo ldconfig

# Now install gnuplot
# Update 2009 Sep 23: The same instructions also work for v4.2.6
# 
cd ~/src
mkdir -p ~/installed/gnuplot-4.2.4
tar -zxf gnuplot-4.2.4.tar.gz
cd gnuplot-4.2.4/
 ./configure --prefix=/home/dmaitra/installed/gnuplot-4.2.4 \
             --with-readline=gnu
 make
 make install

cd ~/src/
ln -s /home/dmaitra/installed/gnuplot-4.2.6/bin/gnuplot
rm -rf PDFlib-Lite-7.0.3* gnuplot-4.2.4*

## Edit ~/.bashrc and add gnuplot alias:
#alias gnuplot="gnuplot -bg white"

3.3 Install cfitsio (click to show)

 cd src/
 wget ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio3130.tar.gz
 tar -zxf cfitsio3130.tar.gz
 mkdir -p /home/dmaitra/installed/cfitsio3130
 cd cfitsio/
  ./configure CC=gcc --prefix=/home/dmaitra/installed/cfitsio3130
  make shared
  make install
  make testprog
  ./testprog > testprog.lis
  diff testprog.lis testprog.out # Output should be nothing
  cmp testprog.fit testprog.std  # Output should be nothing
 cd /home/dmaitra/src/
 rm -rf cfitsio*

## Added in .bashrc For CFITSIO
#C_INCLUDE_PATH=/home/dmaitra/installed/cfitsio3130/include
#LIBRARY_PATH=/home/dmaitra/installed/cfitsio3130/lib
#export C_INCLUDE_PATH LIBRARY_PATH

3.4 Install pgplot (click to show)

cd ~/src/
wget ftp://ftp.astro.caltech.edu/pub/pgplot/pgplot5.2.tar.gz
tar -zxf pgplot5.2.tar.gz
mkdir ~/installed/pgplot5.2
cd ~/installed/pgplot5.2

# Edit the drivers.list or (just for me)
scp akash:/home/dmaitra/installed/pgplot5.2/drivers.list .
# or
# wget http://astrokubuntu.wikidot.com/local--files/start/drivers.list

 ~/src/pgplot/makemake ~/src/pgplot linux g77_gcc
# Edit ~/installed/pgplot/makefile according to the directions in
# http://www.dur.ac.uk/physics.astrolab/ppgplot.html
# Basically:
# Replace "FCOMPL=g77"       in line 25
#   by    "FCOMPL=gfortran"
#
# Replace "FFLAGC=-u -Wall -fPIC -O" in line 26
#   by    "FFLAGC=-ffixed-form -ffixed-line-length-none -u -Wall -fPIC -O"
# Go to ~line 880 and replace
#     "pndriv.o : ./png.h ./pngconf.h ./zlib.h ./zconf.h"
# by  "pndriv.o : "

 make
 make libpgplot.so # Probably not needed because it said that libpgplot.so
                   # was already up to date.
 make cpg
 make clean

rm -rf ~/src/pgplot/

## Edit ~/.bashrc
# PGPLOT_DIR="/home/dmaitra/installed/pgplot5.2"
# export PGPLOT_DIR
#
# Modify LD_LIBRARY_PATH for various softwares
#LD_LIBRARY_PATH=/home/dmaitra/installed/pgplot5.2:$LD_LIBRARY_PATH
#export LD_LIBRARY_PATH

3.5 Install s-lang (click to show)

# Make sure to use the same set of compilers used to build heasoft
CXX=g++ ; export CXX
CC=gcc ; export CC
FC=gfortran ; export FC

cd ~/src/slang-2.2.1/
mkdir ~/installed/slang-2.2.1
./configure --prefix=/home/dmaitra/installed/slang-2.2.1
make
make runtests
make install
sudo ldconfig
ln -s ~/installed/slang-2.2.1/bin/slsh ~/bin/

3.6 Install heasoft and calibration database (click to show)

(A) Install the software

Get the gzipped tar source archive from download webpage for all missions.

# (Actually these are already included in the long
# sudo aptitude install command above)
sudo aptitude install gfortran g++ libncurses5-dev \
 x-dev libx11-dev libxt-dev

#
# Now to heasoft install
# 
CXX=g++ ; export CXX
CC=gcc ; export CC
FC=gfortran ; export FC

cd heasoft-6.7/BUILD_DIR/
mkdir ~/installed/heasoft-6.7

./configure --prefix=/home/dmaitra/installed/heasoft-6.7 > config.out 2>&1 &

grep "\*\*\*" config.out           # Check config.out has no problems

make > build.log 2>&1 &

grep "\*\*\*" build.log            # Check build.log has no problems

make install > install.log 2>&1 &

grep "\*\*\*" install.log          # Check install.log has no problems

# Edit ~/.bashrc to add heasoft initialization lines
HEADAS=/home/dmaitra/installed/heasoft6.6.1/i686-pc-linux-gnu-libc2.8.90
export HEADAS
alias heainit=". $HEADAS/headas-init.sh"
PGPLOT_TYPE=/xw ; export PGPLOT_TYPE

UPDATE on 20090422: I was having some problems running xrtexpomap and decided to upgrade to v6.6.2. I followed the same set of instructions as above, but only with 6.6.1 changed to 6.6.2. The installation went smoothly and the xrtexpomap problem is now gone. I also received an email from Milvia Capalbi and Matteo Perri just around the same time when the latest version was being installed. Milvia and Matteo suggest the following (for Ubuntu OSs)

# BEFORE the initial build of HEASoft.

# for bash
export CFLAGS="-fno-stack-protector"
export CXXFLAGS="-fno-stack-protector"

#or for tcsh:
setenv CFLAGS "-fno-stack-protector"
setenv CXXFLAGS "-fno-stack-protector"

# Following the two above commands, it is possible to launch the usual
./configure
./hmake 
./hmake install

Since xrtexpomap is running with the latest version, I haven't tried recompiling with "-fno-stack-protector" flags yet, but if something fails again I'll give this a try!

(B) Install the calibration database

mkdir ~/installed/caldb
cd ~/installed/caldb/
wget http://heasarc.gsfc.nasa.gov/FTP/caldb/software/tools/caldb_setup_files.tar.Z
tar -zxf caldb_setup_files.tar.Z
# Edit the software/tools/caldbinit.sh and .bashrc to point towards the
# right path to caldb directory.

# Open a new terminal window
heainit
cd $CALDB
wget http://heasarc.gsfc.nasa.gov/FTP/caldb/data/xte/pca/goodfiles_xte_pca.tar.Z
wget http://heasarc.gsfc.nasa.gov/FTP/caldb/data/xte/hexte/goodfiles_xte_hexte.tar.Z
wget http://heasarc.gsfc.nasa.gov/FTP/caldb/data/swift/xrt/goodfiles_swift_xrt.tar.Z
tar -zxf goodfiles_xte_pca.tar.Z
caldbinfo INST XTE PCA
tar -zxf goodfiles_xte_hexte.tar.Z
caldbinfo INST XTE HEXTE
tar -zxf goodfiles_swift_xrt.tar.Z
caldbinfo INST SWIFT XRT
rm -i *tar*

3.7 Install isis (click to show)

# Make sure to use the same set of compilers used to build s-lang and heasoft
CXX=g++ ; export CXX
CC=gcc ; export CC
FC=gfortran ; export FC

cd ~/src/isis-1.5.0-7/
mkdir -p ~/installed/isis-1.5.0-7
unset LD_LIBRARY_PATH

./configure --prefix=/home/dmaitra/installed/isis-1.5.0-7 \
           --with-slang=/home/dmaitra/installed/slang-2.2.1 \
           --with-headas=$HEADAS
make
make check
make install

ln -s ~/installed/isis-1.5.0-7/isis/1.5.0/bin/* ~/bin/

3.7.1 Install slang-gsl module (click to show)

cd ~/src/
wget http://space.mit.edu/CXC/software/slang/modules/gsl/src/slgsl-0.7.0.tar.gz
tar -zxf slgsl-0.7.0.tar.gz
cd slgsl-0.7.0

  ./configure --prefix=/home/dmaitra/installed/slang-2.1.4 \
        --with-slang=/home/dmaitra/installed/slang-2.1.4
  make
  make install

cd ~/src/
rm -rf slgsl-0.7.0*

3.8 Install slirp (click to show)

CXX=g++ ; export CXX
CC=gcc ; export CC
FC=gfortran ; export FC

cd ~/src/slirp-1.9.7/
mkdir -p ~/installed/slirp-1.9.7

./configure --prefix=/home/dmaitra/installed/slirp-1.9.7 
   --with-slang=/home/dmaitra/installed/slang-2.2.1
make
make install
ln -s ~/installed/slirp-1.9.7/bin/* ~/bin/

3.9 Install IRAF (click to show)

(works as of 2015 Jan 14)

Download the ISO image from [http://www.astrosen.unam.mx/~favilac/IRAF/14.04/IRAFv216_64BITS.iso]

Then extract files from ISO either using "Archive Manager", or along the following lines:

mkdir ~/iso
sudo mount -o loop path/to/iso/file/YOUR_ISO_FILE.ISO ~/iso
cd ~/iso

Now install IRAF as root

sudo -s     # Become root
sh install64.sh     # install IRAF
exit     # Become normal user

# Don't forget to unmount
cd 
sudo umount ~/iso

Before using IRAF for the first time

mkdir ~/iraf/
cd ~/iraf/
mkiraf # choose xgterm

Not only does it install IRAF, but also quite a few other useful stuff. E.g. doing 'ls /iraf/extern/' shows the following:

color  fitsutil  guiapps  pyraf  stsdas  tables  telarchive  wcstools  x11iraf

To use IRAF, go to the ~/iraf directory and type

cl

According to the installation script another way to start IRAF could be

A script called iraf has been installed in /usr/local/bin/ which executes the xgterm terminal running ecl, and the ds9 viewer

3.10 Install AIPS [Thanks to Atish Vyas for the instructions] (click to show)

AIPS installation requires libg2c which does not normally come with intrepid (8.10), so

 sudo aptitude install libg2c0

The command below will download and install, along with other dependencies,
the 'XShm.h' header file. This is required to build the XAS program which is used
by the AIPS TV. Without this the AIPS TV will not work.

sudo aptitude install xorg-dev ncurses-dev

Then download the AIPS installation files:

cd ~/src
# Keep both the downloaded files (31DEC09.tar.gz and install.pl) in this directory (~/src)
wget ftp://ftp.aoc.nrao.edu/pub/software/aips/31DEC09/31DEC09.tar.gz
wget ftp://ftp.aoc.nrao.edu/pub/software/aips/31DEC09/install.pl
# Create a directory where you wish to install aips
mkdir -p ~/installed/aips/

#Start aips installation
perl install.pl

The perl script install.pl will unpack the tarball 31DEC09.tar.gz and will start installation. Follow the questions asked during the process (and of course answer them for proper installation).

Finally edit the file "/etc/services" to add following lines :

# Local services

sssin           5000/tcp        SSSIN      # AIPS TV server
ssslock         5002/tcp        SSSLOCK    # AIPS TV Lock
msgserv         5008/tcp        MSGSERV    # AIPS Message Server
tekserv         5009/tcp        TEKSERV    # AIPS TekServer
aipsmt0         5010/tcp        AIPSMT0    # AIPS remote FITS disk access
aipsmt1         5011/tcp        AIPSMT1    # AIPS remote tape 1
aipsmt2         5012/tcp        AIPSMT2    # AIPS remote tape 2
aipsmt3         5013/tcp        AIPSMT3
aipsmt4         5014/tcp        AIPSMT4
aipsmt5         5015/tcp        AIPSMT5
aipsmt6         5016/tcp        AIPSMT6
aipsmt7         5017/tcp        AIPSMT7

To start aips use command

aips

For binary installation

perl install.pl -n

3.11 Install SExtractor (click to show)

As of writing (2009-APR-07) the version of sextractor installed automatically by Ubuntu via 'sudo aptitude install sextractor' is buggy. Therefore I had to resort to installing it manually. These are the steps:

cd ~/src/
wget ftp://ftp.iap.fr/pub/from_users/bertin/sextractor/sextractor-2.5.0.tar.gz
tar -zxf sextractor-2.5.0.tar.gz 
mkdir -p ~/installed/sextractor-2.5.0
cd sextractor-2.5.0/
  ./configure --prefix=/home/dmaitra/installed/sextractor-2.5.0
  make
  make install
  cd ~/src
rm -rf sextractor-2.5.0*

# Add to $PATH in .bashrc
# export PATH="$PATH:$HOME/installed/sextractor-2.5.0/bin"

3.12 Install  mpeg2encode (click to show)

# Get the tarball:
wget http://www.mpeg.org/pub_ftp/mpeg/mssg/mpeg2vidcodec_v12.tar.gz
tar -zxf mpeg2vidcodec_v12.tar.gz
cd mpeg2/
 make
 cp ./src/mpeg2enc/mpeg2encode ~/bin/
 cp ./src/mpeg2dec/mpeg2decode ~/bin/

cd ../
rm -rf mpeg2/ mpeg2vidcodec_v12.tar.gz

3.13 Paolo's eqpair model (click to show)

mkdir $HOME/src/eqpair
cd $HOME/src/eqpair
tar -zxf /path/to/eqpair.tar.gz

# Edit lmodel.dat to keep only the model parameters for eqpair
# Edit xseqpair.f to point DATADIR (line 838 in my version) to //full path// to 
# where $LMODDIR in .bashrc points, e.g. /home/dmaitra/src/eqpair

heainit
xspec
XSPEC12> initpackage eqpair lmodel.dat /home/dmaitra/src/eqpair
XSPEC12> tclexit

# Edit .bashrc to set $LMODDIR pointing to /home/dmaitra/src/eqpair
# LMODDIR=$HOME/src/eqpair ; export LMODDIR

Now eqpair can be loaded from inside XSPEC as follows

XSPEC12>lmod eqpair /home/dmaitra/src/eqpair

# To check that the model was loaded properly type

XSPEC12> model eqpair

# and hit enter to accept all the default parameter values

If $LMODDIR is defined properly, ISIS should load eqpair when you do a " require("xspec"); ". Check for a line like "loading /home/dmaitra/src/eqpair/libeqpair.so" as ISIS starts up.

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4. Setting up Panotools (autopano, hugin, enblend etc.)

+ click to show

While most of the pano tools can be installed via aptitude, it may be better to get the bleeding edge. I followed the directions on this webpage http://wiki.panotools.org/Hugin_Compiling_Ubuntu (accessed 2009 Feb 16)

Note added on 2009 Feb 25: At least one of the problems with getting via aptitude is that hugin 0.7 needs enblend 3.2 (which contains 'enfuse') but installs enblend 3.0 (which does not contain enfuse). This could be fixed by replacing enfuse by enblend in preferences (Bug 303222, accessed on 2009 Feb 25).

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5. Setting up UvA printers, scanners and draadloos

+ click to show

Printers: CUPS configuration following email from Evert Rol (on Tue, Apr 28, 2009) and some poking around

The colour printer (p001004):
5.1.1 Open firefox and go to http://localhost:631/ and click "Add Printer"
5.1.2 Name: p001004 ; Location: Infotec ISC 3535, C4.42; Description: Color printer; and click continue
5.1.3 Device: LPD/LPR Host or Printer
5.1.4 Device URI: lpd://wtcw-server.science.uva.nl/p001004
5.1.5 Use the custom PPD file http://www.openprinting.org/foomatic-db/db/source/PPD/Infotec/PS/Infotec-ISC_3535_PS.ppd
5.1.6 Print a test page to make sure everything is working properly

The b/w printer (p001007):
5.1.1 Open firefox and go to http://localhost:631/ and click "Add Printer"
5.1.2 Name: p001007 ; Location:Infotec IS 2145 PS, C1-2.17-05 ; Description: BW printer; and click continue
5.1.3 Device: LPD/LPR Host or Printer
5.1.4 Device URI: lpd://wtcw-server.science.uva.nl/p001007
5.1.5 Use the custom PPD file http://www.openprinting.org/foomatic-db/db/source/PPD/Infotec/PS/Infotec-IS_2145_PS.ppd
5.1.6 Print a test page to make sure everything is working properly

To print from command line try

lpr -P p00100[4/7] <filename>

Scanner: Following Atish's email on Mon, May 18, 2009

1] press key 'scanner' [from among the choices 'printer', 'copy', 'document server'…on the left hand side of the printer]

2] place the document to be scanned (the side to be scanned facing the glass), close the lid.

3] press 'manual-entry' key appearing on the printer screen….a virtual key board will appear on the screen. Type in your email ID there. You can use e-mail ID outside the institute domains such as moc.liamg|zyx#moc.liamg|zyx or moc.gnihtyna|zyx#moc.gnihtyna|zyx……press OK

4] press 'scan settings' on the screen : here you can choose resolution, colour scheme, page size & layout, etc. (The default setting is 'auto-detect' which works perfect).

5] press 'the biggest green key' on the printer key board [it is on the right hand side of the printer screen].

6] After a quick scanning (perhaps in a second) a message will appear on the screen asking you to replace the document with another one, if you have, within next 60 seconds. (Which means you can scan multiple documents one by one and have them all in one attachment). Repeat this step for all the documents you have.

7] press '#' key on the printer's number key pad.

8] Check your email…you should have the attachment by now..:-)

Wireless: Following Hendrik's email (which was in turn forwarded by Eva van der Linden on Mon, May 11, 2009)

In order to follow Hendrik's email, you will need to have nm-applet installed ('sudo aptitude install nm-applet' or some similar incantation). Once you have nm-applet up and running, just follow Hendrik's email below

To get wireless working under linux, it is very likely that you have to deal 
with NetworkManager, as it is common to recent versions of both Fedora 
and Ubuntu. Take the following steps:

- rightclick on the applet in the system tray
- click 'Edit connections'
- add a wireless connection
- set connection name to eduroam
- enable 'connect automatically'

I then have three tabs visible: Wireless, Wireless Security and 
IPv4 Settings. In Wireless my settings are as follows:

SSID: eduroam
Mode: Infrastructure
BSSID: (blank)
MAC Address (blank)
MTU: automatic

In Wireless Security: (!) marks settings different from web-guide 
science department

Security: WPA & WPA2 Enterprise
Authentication: Tunneled TLS (i.e. TTLS)
Anonymous Identity: (blank) (!)
CA Certificate: (none) (!)
Inner authentication: PAP
user name: [e-mail] (substitute with your own, of course. 
Don't forget the number and/or @uva.nl. It's your 'zelfbediening' login)
Password: your zelfbediening password

in IPv4 settings:
Method: Automatic (DHCP)
(basically don't set anything in IPv4 settings)

Notes: NetworkManager shows the available networks when you left click 
on the tray icon. It is likely that connection by clicking on the tray icon does 
not work. You should really follow the route above. Also note that we did 
not supply a cert (.pem, .der, .whatever) file. This may cause the computer 
to complain, but you can safely ignore those complaints.

6. Setting up Heasoft/ISIS on a Mac OS X (v10.5.8)

+ click to show

2009/09/21 : After a few emails with John Houck I found that probably the only uniform compiler set that installs both Heasoft and ISIS in Macs are the gcc/gfortran-4.4 binaries provided by the HPC page. Also thanks to the newly updated ISIS installation page, I realized I could skip installing both Pgplot and cfitsio and use the heasoft installed ones.

Another important thing to keep in mind is the bug in XSPEC gaussian model for 64-bit systems, which Mike Noble found (emailed me on Wed, Mar 12, 2008). Here's what he instructed:
Edit the heasoft-6.7/Xspec/src/XSFunctions/xsgaul.f to change the erf() declaration from

external erf
to
intrinsic erf

So here's what I did, which installs both heasoft, s-lang and isis:

# Installed gcc/gfortran from HPC in /usr/local/bin

CXX=/usr/local/bin/g++ ; export CXX
CC=/usr/local/bin/gcc ; export CC
FC=/usr/local/bin/gfortran ; export FC

#
# Install Heasoft
# 
cd ~/Downloads/
tar -xf heasoft6.7src.tar
gvim heasoft-6.7/Xspec/src/XSFunctions/xsgaul.f  # Make changes suggested by Mike
cd heasoft-6.7/BUILD_DIR/

./configure --prefix=/Users/dmaitra/installed/heasoft-6.7 >& config.out &
grep "\*\*\*" config.out          # No errors found
make >& build.log &
grep "\*\*\*" build.log           # No errors found but some warnings!
make install >& install.log &
grep "\*\*\*" install.log         # No errors found

gvim ~/.bashrc                     #  Set proper heasoft environment

#
# Install s-lang
#
cd Downloads/slang-2.2.1/
mkdir -p ~/installed/slang-2.2.1

./configure --prefix=/Users/dmaitra/installed/slang-2.2.1
make
make runtests
make install

cd ../
rm -rf slang-2.2.1/
ln -s /Users/dmaitra/installed/slang-2.2.1/bin/slsh ~/bin/

# 
# Install ISIS
#
cd Downloads/isis-1.5.0-7/
mkdir -p ~/installed/isis-1.5.0-7

./configure --prefix=/Users/dmaitra/installed/isis-1.5.0-7    \
            --with-slang=/Users/dmaitra/installed/slang-2.2.1 \
            --with-headas=$HEADAS 
make >& build.log & 
make check >& make_check.log &
make install >& make_install.log &

cd ../
rm -rf isis-1.5.0-7
ln -s /Users/dmaitra/installed/isis-1.5.0-7/isis/1.5.0/bin/isis \
      /Users/dmaitra/bin/

Note that the heasoft build.log will contain many instances of *** as the check with "grep "\*\*\*" build.log" will show. However, according to John Houck "Those warnings aren't important. gcc-4.4 is just unusually strict about how the 'const' qualifier is used."

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7. image analysis tips

click to show

Create a high quality PNG from PS

convert -density 400 lc.ps -rotate 90 -flatten -resize 25% lc.png

Add a caption/label inside an image

convert ip.JPG -gravity Northeast -stroke white -fill white -pointsize 60 -annotate +50+20 'Label \@ pos' -flatten op.JPG

Extract a linear 16 bit tiff from a raw image using dcraw

dcraw -j -4 -T <RAW_file_name>

8096—8099 are darks, so average them to get a master dark.

convert IMG_8096.JPG.png IMG_8097.JPG.png IMG_8098.JPG.png IMG_8099.JPG.png \
   -average master_dark.png

Remove master dark from all frames

convert -compose minus -composite master_dark.png IMG_8094.JPG.png \
  ds.IMG_8094.JPG.png

Compose a bunch of images to create a star-trail (based on http://www.wizards-toolkit.org/discourse-server/viewtopic.php?f=1&t=12040#p39496)

convert image1 image2 -compose lighten -composite result
convert result image3 -compose lighten -composite result
etc

To split a JPG (and possibly PNG, TIFF etc. too) into 3 r,g,b FITS files

convert ip.jpg -channel red -fx "u.r" -channel green -fx "u.r" -channel blue -fx "u.r" r.fits
convert ip.jpg -channel red -fx "u.g" -channel green -fx "u.g" -channel blue -fx "u.g" g.fits
convert ip.jpg -channel red -fx "u.b" -channel green -fx "u.b" -channel blue -fx "u.b" b.fits

To create a lossless movie from a bunch of PNGs using mencoder (based on http://lists.mplayerhq.hu/pipermail/mencoder-users/2005-December/002323.html retrieved on 2012 Sep 06)

mencoder "mf://*.png" -mf fps=2.0:type=png:w=900:h=900 -ffourcc MPNG -ovc copy -force-avi-aspect 1.0 -nosound -o result.avi

obviously change the fps value, the w/h (width/height of input PNGs), and the aspect ratio of the output avi!

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8. latex/dvips random stumbles

click to show

dvips mapping of a certain font (like Symbol or Helvetica) as not found.

See http://www.grassbook.org/neteler/highres_pdf.html

emulateapj needs revtex4:

sudo apt-get install texlive-publishers

9. Tips & tricks

click to show

Install aperture photometry tool (APT) from http://www.aperturephotometry.org/

Make sure you have JRE (In ubuntu 14.04 a 'sudo apt-get install default-jre' does the trick). Download the gzipped tarball from their webpage. Open it in, say, ~/installed/. Then add the following lines to ~/.profile

export APT_HOME=$HOME/installed/APT_v2.4.7
export PATH=$APT_HOME:$PATH
export APT_ARCH=LINUX

Concatenate PDFs:

pdftk 1.pdf 2.pdf 3.pdf cat output merged.pdf

(For more options see: http://www.ubuntuhowtos.com/howtos/merge_pdf_files (accessed 2014 June 11))

Copy contents of a folder recursively, keeping symlinks, to another machine

tar -c mydir/ | ssh -C username@machine "tar -C /path/to/dest/ -x"

(based on http://directed-procrastination.blogspot.com/2010/10/scp-and-symlinks.html accessed 2015 Feb 23)
Use wget to recursively get contents of a webpage

wget -e robots=off -rH -l <levels> -np www.blah.edu/path/to/some/directory

(See e.g. http://stackoverflow.com/questions/15434173/wget-downloads-only-one-index-html-file-instead-of-other-some-500-html-files (accessed 2014 June 19))

Use wget to download only certain files from a password protected site, e.g. to download all filenames matching 150308 from ftp://myserver.nonexistent/pub/myfiles/

wget -rH -nd -A "*150308*" --user=<username> --password=<topsecret> ftp://myserver.nonexistent/pub/myfiles/

Based on http://www.gnu.org/software/wget/manual/html_node/Recursive-Retrieval-Options.html and http://askubuntu.com/questions/29079/how-do-i-provide-a-username-and-password-to-wget (accessed 2015 Mar 10)

Bash read multi-column ASCII file line by line with different columns as different variables

Contents of a sample file called test.txt

a11 a12 a13 a14
a21 a22 a23 a24
a31 a32 a33 a34

The following script will print the second and fourth columns of test.txt

while read -r c1 c2 c3 c4; do
    echo $c2 $c4
done < test.txt

(From http://stackoverflow.com/questions/15442220/pipe-file-line-by-line-into-multiple-read-variables/ accessed on 2014 Jul 07).

Astrometry.net software. Only v0.43 would work. Newer doesn't!!! Install steps

    tar -zxf astrometry.net-0.43.tar.gz 
    cd astrometry.net-0.43/
    make
    make py
    make extra
    make install INSTALL_DIR=/home/ast/installed/astrometry.net-0.43

Center on certain RA, Dec in a plate-solved fits image and save as a png image

ds9 <ip.fits> -zscale -align yes -geometry 640x480 -view colorbar no -view panner no \
  -view info no -view magnifier no -view buttons no -zoom 0.5 \
 -pan to 20:24:03.83 +33:52:02.2 wcs fk5 \
 -saveimage png op.png

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This page was created by Dipankar Maitra, in an attempt to learn some of the wiki-lingo.

Comments are welcome. You can reach me at: ddotmaitra AT gmail . com