Urania

A blog named for the muse of Astronomy containing musings by an astronomer

Archive for the ‘SciSoft OSX’


Scisoft OSX 2011.4.1beta available and IRAF as a package install from STScI! 0

Posted on May 24, 2011 by Juan

New version of Scisoft OSX 64-bit beta available

I just noticed today that, over a month ago, Nor Pirzkal placed a new beta of the 64-bit SciSoft OSX online here.  I have not had as much joy with the 64-bit version of IRAF as with the older ones.  That said, this version of SciSoft OSX doesn’t install over the old 32-bit version, so a simple edit of your start up files can allow you to switch between the two versions.

I backed up the old version of scisoft using the command line

sudo mv /usr/local/scisoft /usr/local/scisoft_old

and then I installed this version

sudo tar -C / -xzvf scisoft.current.tar.gz

(you may not need to ‘sudo’ if you have write permission for /usr/local).  I’ll report back if anything interesting changes.  The CONTENTS file only noted that ncftp 3.2.5 had been added.  Not sure why an FTP client was added unless it was needed by some other package.

One note is that I have been experimenting with Enthought’s Python Distribution and have it over-riding the python packages installed by the Scisoft OSX installation, so I may have to play around a bit to get PyRAF working again.  Or I may drop SciSoft OSX altogether (since its Python interferes with Enthought).

STScI makes MacOS X Package Installer version of IRAF available

In the process of looking at PyRAF, I was pleasantly surprised to find that STScI now has a package installer available for installing IRAF+STSDAS/TABLES and all the corresponding files needed for STSCI Python in a single click.  It is only for 64-bit Macs.  I will have to look this over in the future, but it apparently installs everything in /usr/scisoft so it will not collide with anything. However, it also requires a new installation of gfortran which I already know can break my PGPLOT installation.

Playing with Scisoft OSX 2011.1.1 beta 0

Posted on March 03, 2011 by Juan

Since I am on sabbatical, I have been working on updating some of my software.  One of my projects is to update External SPECROAD to be functional on 64-bit IRAF installations which are becoming more common.  To do this, I needed to get a 64-bit IRAF installation.  Lucky for me, Nor Pirzkal has been working on updating Scisoft OSX for 64-bit and the most recent beta version is very usable.

Dr. Pirzkal started work on this version in early 2010.  The first alpha release was in March 2010 and contained the following note:

The latest version Scisoft OSX is being prepared. We are switching the distribution to be 10.6 compatible only. Its location is also being moved (again) from /Applications/Scisoft/ to /usr/local/scisoft/.
The main changes to this version are:

1) Requires OSX 10.6
2) 64 bit only
3) Now uses the OSX Python system
4) Pyraf no longer uses X11 and all windowing calls are made using the OSX Aqua TCL/TK libraries

These all sounded good to me, especially the move away from using a custom python installation.  The only problem is that the alpha was missing a lot for me, so after an initial try, I dropped it and went back to the 32-bit Scisoft OSX 2009.10.1.

This version installed easily enough with a couple of clicks to uncompress the ZIP file and then another click on the resulting package file to trigger the Mac installer.  The instructions were straight forward for how to edit your environment.  Once done, I had Scisoft OSX installed in /usr/local/scisoft/. I’ll note that this doesn’t clobber any previous installations of Scisoft OSX, so it is easy to switch back by editing your startup files. I am presenting a slightly modified version of his checklist for upgrading here.

  1. Install Scisoft OSX 2011.1.1b by downloading it here or from my mirror (NOTE: The file is misnamed Scisoft_OSX_macintel_2011.11.1b.pkg.zip, don’t worry, you don’t need to time travel to use this version before November 2011).
  2. Download the patch to IRAF 2.15.1a at
    ftp://iraf.noao.edu/iraf/v215/PCIX/patch1.macx.x86_64.gz(for 64 bit systems).
  3. In a terminal, type: cd /usr/local/scisoft/packages/iraf/iraf
  4. Assuming the downloaded file ended up in ~/Download, type
    sudo tar xvfz ~/Downloads/patch1.macx.x86_64.gz
  5. Now IRAF should show that you are using v2.15.1 (not 2.15) when you start it. However, that is not all: also the external packages need to be updated. I found the instructions on the IRAF web page not applicable for the Scisoft OSX installation. Instead, 
    1. start a superuser shell:
      sudo tcsh
    2. source /usr/local/scisoft/bin/Setup.csh
    3. cd to a directory containing your login.cl (might also work without this step) and type ecl
    4. within IRAF:
      cd /usr/local/scisoft/packages/iraf/iraf
    5. And then type:
      make update
      (and have a coffee or three because this is taking a while)
  6. logout (of IRAF) and then exit (to make sure you’re not continuing with superuser privileges

That process worked fine for me and I now have a current IRAF installation.  There are a few things in this beta that are not noted in the CONTENT file that came with it.  It certainly contains sextractor 2.5.0 (the current version is 2.8.6) which isn’t listed in the CONTENT file and in addition to STSDAS and TABLES 3.13, which are noted in the CONTENT file, the following IRAF packages are preinstalled:

  • color 2.0
  • fitsutil
  • gemini 1.9
  • gmisc
  • guiapps 1.2
  • mscred 4.8
  • rvsao 2.7.8  (this is the current version as far as I can tell)
  • nlocal
  • nmisc
  • vol 2.8

 

Mac Apps for the Professional Astronomer 2

Posted on June 01, 2010 by Juan

I was asked by one of my colleagues who was late to switching to a Mac (from linux) what the necessary software is for an astronomer to have on their Macintosh. Some lists of this sort have been assembled online, however most are no longer available. Some resources I was aware of that were still online as of this writing (Summer 2010) were

  • Jane Rigby’s (Carnegie Observatories) OS X for Astronomers: This site is a fairly complete listing of Mac software the Professional Astronomer would be listed in. However, she uses “Fink” whereas I prefer “MacPorts”. To each their own.
  • MacOS X for Astrophysicists: This site is a bit dated (last update 2007) but there is a lot good information about how to configure X11, LaTeX, etc. on the Mac.
  • MacResearch: Focused more generally on using a Mac for research (notably programming), this site is a good read even if not astronomy focused.

My approach here will be to list everything I use on a regularly basis in my research. I will warn you up front that I am an optical astronomer who as dabbled in some radio astronomy, but I don’t know anything about High-Energy packages. So that is one bias. Secondly, being a college professor at a smaller state institution, I tend to focus on free (as in beer) or inexpensive software although I will list a few programs that I think are definitely worth the money for professional astronomer.

Programming/Unix Environment

There is some stuff any astronomer using a Mac should install, because it is free and/or critical to using your computer as a competent astronomer (depending on your specialty)…

  • XCode: You will need the gcc compilers in many cases and they come with the OS, so you might as well install them. If you want to get the most current Xcode, you can download it from the Apple Developer Connection website (you will need a free account).
  • g77/gfortran compilers: If you need a g77 (for MacOS before 10.6) or gfortran compiler, the best place to get pre-built binaries is at the High Performance Computing of MacOS X website.
  • X11: X11 is an optional install under Tiger and is installed by default under Leopard. However, when in Leopard, Apple switched from Xfree86 to X.org, and this transition introduced some advantages (no DISPLAY environment setup necessary…. yeah!) and some bugs (Boo!). As such, I had been using XQuartz in Leopard, which remain a few steps ahead of Leopard’s X11 and easily installed over it. However, I have found Snow Leopard’s X11 installation stable and robust enough to not replace it with XQuartz any more.
  • MacPorts: The bane of many unix-style OSes these days is the package manager one uses to install the unix-style programs with all their dependencies. I have settled on MacPorts. I used it’s “competitor” Fink for a while, but I have found MacPorts to generally be a much more up-to-date package manager. I use it to install TeTeX and a multitude of CLI programs (PGPLOT, gs,gv,gsl,xephem).
    • Porticus: is a decent (free) GUI front end for MacPorts if you fear the command line.

For the Optical Astronomer

This is the data reduction software I use almost every time I work on my research…

  • Scisoft OSX (My Mirror): IMHO the simplest way to install IRAF and many other packages I use regularly (PGPLOT, WCSTools, Sextractor, CFITSIO, etc.) in one double-click of a mouse (and some editing of my .tcshrc file).
  • SAOImage DS9: I sometimes update the version of DS9 included in SciSoft OSX with the most current versions from the CfA.
  • HEASARC’s fv: They call it the “Interactive FITS File Editor” and frankly it sometimes is the easiest way to quickly see the contents of a complex FITS files.
  • JSkyCalc: This venerable observing planning software that used to be solely for the command line (when it was skycalc) has now been updated to a graphical user interface written in java, so it runs on almost any platform, including Mac OSX. For the Mac, just save the jskycalc.jar file someplace and double click on it to launch it.
  • IDL: Definitely not cheaper (but cheaper than it used to be). Some astronomers I know swear by it (I have been known to swear at it). Personally, I do need the power of IDL sometimes, especially when someone else provides me her/his IDL code. If you use it, you will probably want to grab the IDL Astronomy Users Library which provides a large number of pre-built IDL routines for the astronomer. If you are feeling cheap, you might be able to get away with GDL (from High Performance Computing)

For the Radio Astronomer

This is the data reduction software I played around with when reducing radio data. I can’t claim I am current on the state of the art, so let me know if you feel I am missing something here.

  • AIPS: When I was doing more radio astronomy, I was working with AIPS a lot. I helped in the process of getting it working under MacOS (as a guinea pig). It ran quite nicely under MacOS the last time I used it (about 2004).
  • CASA: CASA (formerly AIPS++) is a sort of successor to AIPS. Personally, I was never that impressed with it, but I know several people who like using it (such as folks involved with ALMA). It is available for Mac OS 10.5 and 10.6 (Intel Macs only).

Writing Tools for Astronomers

Writing either documentation or papers for peer-review publications can be a challenge. For informal work, I have quite happy using Apple’s Pages for written work or Apple’s Keynote when assembling a poster or set of slides. However, for peer-reviewed journals or NSF applications, I typically use latex, having installed tetex with MacPorts.

  • Texmaker: is a nice interface for writing LaTeX on the Mac. Certainly not perfect or as good as some commercial products I have seen, but it is free and it works well. I especially like it when used with the Skim PDF reader which allows in-window updating of the PDF.
  • Papers: This is an awesome package for organizing your personal library of publications. It provides (somewhat glitchy) ADS Abstracts and arXiv interfaces that allow you to match PDF files to their metadata. Once you have done this, you can search for you local library by the words in the title, abstract, author’s name, year of publication, etc. And you can keep your PDFs organized. It has been a wonderful way for me to keep track of everything I have been reading when I have to prepare a paper.
  • iWork: is a very useful package from Apple that acts as a lower cost replacement to Microsoft Office (if all I cared about were cost, I would use OpenOffice.org). However, I use it because it includes:
    • Keynote: Keynote is a much more polished presentation manager than PowerPoint.
    • Pages: I prefer pages for my word processing and MacResearch had a compelling article on why you might use Pages for grant applications.
  • MathType 6: I would recommend also getting MathType 6, which let’s you insert equations into Pages or Keynote with ease (and it accepts LaTeX as a way of building equations). Make sure to update to the current version, it avoids a lot of crashing bugs.
  • LaTeXit: If you don’t want to pay for a commercial program, LaTeXit is a great option for typeseting formulas with LaTeX. It allows you typeset and then drag the results into Keynote or Pages documents where they are inserted as PDF images.
  • Evernote: I don’t use Evernote solely for writing papers, it is just a place to toss little notes I used to keep on post-it notes. But if I want to save some webpage or some text for later use, it is a perfect tool for that. It can sync between Mac and iPhone/iPod touch and it is free for up to 40 MB of notes a month.

Astronomically Useful Widgets

Widgets have been in MacOS since version 10.4 (Tiger), and while I don’t find them terribly useful, there are some free Widgets can be useful to have on observing runs:

  • Clear Sky Clock Widget: I may be biased since I helped re-work this widget and am responsible for the current version, but is useful as a way of displaying the current Clear Sky Chart (formerly called “Clear Sky Clock”) on your desktop. Clear Sky Chart is only useful for astronomers in North America.
  • AstroTimes Widget: I am not sure if this widget is still available, but it was a quick way to see the Local Sidereal Time when observing.

Astronomically Useful Spotlight Plugins

Spotlight is a feature that has been built-in to MacOS X since version 10.4 (Tiger). It indexes the contents of files to allow for almost instantaneous searches of the contents of a hard drive. The built-in plugins search many file types, but the following additional plugins are useful for file formats astronomers commonly run into.

  • FITSImporter: This plugin allows Spotlight to index FITS file headers.

Astronomically Useful QuickLook Plugins

QuickLook is a feature that has been built-in to MacOS X since version 10.5 (Leopard). When in the Finder, selecting a file and tapping on the spacebar displays a preview of the file. As with Spotlight plugins, many common file formats are supported with the built-in plugins, but for file formats astronomers commonly run into some plugins can be useful.

  • QLFits: This QuickLook plugin allows easy previewing of FITS file headers and images/spectra from the Finder.
  • QLColorCode: This QuickLook plugin displays source code files with syntax highlighting making QuickLook a much more powerful way of previewing code.
  • EPSQuickLookPlugIn: Allows viewing of encapsulated PostScript files via QuickLook. Since most figures I embed in my papers start as EPS files, this is very useful to me.

The Less Obvious Stuff

Some software doesn’t fit well into a particular broad class of work astronomers do, but can come in useful all the same for specific tasks.

  • User Interface Enhancements:
    • ShellHere.app: Drag this to your Finder winder and from now on, if you want to open the Terminal at a location corresponding to a given Finder winder, all you you need to do is click on the ShellHere icon. Works great, sort of the counterpart to “open .” in the terminal opening up a Finder window.
    • QuickSilver: Why waste your time digging through the Finder? I use QuickSilver to launch programs, access frequently used documents, and basically streamline my use of my Mac. Its the swiss army chainsaw of launchers.
    • GeekTool: This is an awesome little tool that allows you to display almost anything on your desktop. I use it to display my weblogs and system logs to my desktop, along with the local weather conditions and Doppler radar image. Anything you can display in the shell can display on the desktop.
  • A backup solution beyond Time Machine! Time Machine (part of Mac OS since version 10.5) is wonderful for incremental backups, but if your boot drive fries, you can’t boot from your Time Machine backup. This is why I also clone my boot drive regularly.
    • Carbon Copy Cloner: This is a free way to clone your boot drive on the Mac.
    • DejaVu: If you want an more automated solution, I prefer DejaVu, which runs scheduled rsync sessions in the background. That way, my backup drive is constantly updated and when my boot drive fails, I can just switch over to the backup without losing a beat.
  • Versions: Actually, I can’t say I ‘recommend’ Versions per se. I would strongly recommend subversion or some other version tracking system for anyone who writes code regularly. It makes tracking edits to source code (and latex documents) a breeze. I happen to use Versions as a very nice GUI that allows quick examination of differences between different versions of the source code you have tracked. That said, it is not cheap and I think SynX is a perfectly adequate free GUI front-end for code version tracking with similar functionality, if not as polished.
  • Parallels/VMWare Fusion/VirtualBox: If you occasionally have to run software that only runs on that other platform (you know, Linux), virtualization software is quite useful. I have found both Parallels 5 and VMWare Fusion 3 to be quite good (I found Parallels to be faster, but I heard VMWare was catching up). VirtualBox is free (as in beer) and may be an option to try before shelling out money for commercial virtualization software.
  • Chicken of the VNC: At several observatories, I am required to use VNC to interface with the computers. Chicken of the VNC works as a client. There are commercial VNC clients that are a bit faster, but if you have decent bandwidth, this works fine.
  • Wx: As an frequently optical astronomer, I sometimes obsess about the weather. Of all the weather programs out there, I have found this one to be the most stable and flexible. Its relatively inexpensive ($16.95 US), but as a warning, it is limited to the United States.
  • OmniFocus: This program is probably the single most useful program I have for managing my time. It implements David Allen’s Getting Things Done approach to time management. Its not cheap, nor is it completely intuitive… but it is absolutely necessary for me. A iPhone version also exists, which allows syncing of your OmniFocus sessions between your Mac and iPhone/iPod Touch.
  • DropBox: If you look at DropBox for the first time, it just looks like a way to sync files between computers. That is, until you realize you can allow specific users to share specific directories. I use it to share files to big to email with collaborators all the time. The only warning, it currently doesn’t map out extended attributes of files (like the executable settings) between computers, so it is not good for shell scripts. This failing is supposed to be fixed in the current version 0.8 beta.
  • fseventer is useful for diagnosing programs that create files. It tracks all file system events as long as it is on. So if you want to know where an installer is tossing files around your system, this will help you see what is happening. Its rare that I need it, but when I do, it is a Godsend.

[I made some minor edits adding some links I had forgotten about. – June 1, 2010 11:45 am CDT]

Scisoft OSX 2009.10.1 released 2

Posted on October 01, 2009 by admin

Nor Pirzkal has released another minor update to Scisoft OSX. He states in his blog that:

A minor revision of Scisoft is available for downloading. Many people are experiencing many problems with the Apple Package Installer and I am distributing this release as a simple tar.gz file.

This version of Scisoft is distributed as a simple tar file that can be un-tarred in /. Scisoft expect to be located in /Applications/scisoft/

I can confirm the CONTENTS file distributed with the install is identical to the file for Scisoft 2009.9.1 so this release may just be a way to avoid some issues with the Apple Package Installer program.

This change to a tarball format is good, but it changes how to install the software. However, there is at least one major glitch in this distribution

  • WCSTools is missing from the installation! There are symbolic links to the package, but the /Application/scisoft/i386/Packages/wcstools-3.7.3/ directory is empty! If you are upgrading from a previous version of Scisoft OSX, there is an easy way to recover from this problem. I am outlining my suggested installation routine below.
  • As I noted for Scisoft 2009.9.1, “on Snow Leopard, Gordon Richards discovered that if you attempt ‘import pylab’ in python, you get a bus error. I can confirm the same error occurs on my Snow Leopard machine using either this SciSoft OSX release or the previous one. Furthermore, I can confirm the error DOES NOT occur in Leopard. I am not a heavy Python user, so I will leave it to Gordon, Nor, and others to investigate this issue. Gordon notes that this blog posting contains instructions for getting pylab installed under a vanilla Snow Leopard install, in case you need them.”

My suggested routine for upgrading to this version of Scisoft OSX from a previous version is the following:

  1. Backup the previous version of Scisoft by renaming the /Application/scisoft/ directory to /Application/scisoft_old/.
  2. Download the current gzipped tarball of Scisoft OSX. The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.
  3. Using the command line in an administrative account, you can untar the tarball using the command:
    sudo tar -C / -xzvf Scisoft_OSX_macintel_2009.10.1.tar.gz
    You will be asked for your account password to allow ‘sudo’ to run the tar command as root.
  4. The files are untarred with their ownership intact from when Nor created the tarball, so be sure to change the ownership to match your root account using
    sudo chown -R root:admin /Applications/scisoft/
  5. Finally, if you want to copy over the WCStools package from the previous Scisoft OSX installation, you can use the command:
    sudo cp -r -p /Applications/scisoft_old/i386/Packages/wcstools-3.7.3/ /Applications/scisoft/i386/Packages/wcstools-3.7.3/
    That should get your back the WCStools.

I have alerted Nor to the missing wcstools directory as well as some other minor issues with this release. Hopefully, if Nor has some time, he will make

Scisoft OSX 2009.9.1 released 2

Posted on September 16, 2009 by admin

Nor Pirzkal has released a minor update to Scisoft OSX. He states in his blog that:

This version should fix a few outstanding bugs in version 2009.6.1. People running on case sensitive file system will hopefully stopped having problems. This version otherwise upgrades a few minor packages as described in the NEWS and CONTENTS files.

This version requires OSX Intel 10.5.x or higher. It also works fine with OSX 10.6.0 and OSX 10.6.1.

From reviewing the CONTENTS file distributed with the install, the major changes from the previous version as as he indicated, quite minor. They include:

  • The following Python packages were updated:
    • matplotlib 0.99 (upgraded from version 0.98.5.2)
    • pyraf 1.8 (upgraded to the current release version from version 1.7.1)
    • pygsl 0.9.4 (upgraded from version 0.9.3)
    • mxDateTime 3.1.2 was added to the distribution. Adds certain useful date manipulation functions to the python installation.
    • pysao 2.1.8 was added to the distribution. This appears to add direct XPA communication capability between python scripts and SAOImage DS9.
  • The gsl library was update from version 1.11 to 1.13.
  • [From NEWS file] Changed ds9 [command line] unix version a [symbolic] link from an alias. I noticed the SAOImage DS9 website currently says “Note: the next release of DS9, version 5.7, will be available October 15th.”
  • [From NEWS file] Fixed references to “packages” to “Packages” in Setup scripts

The glitches I have noticed in this distribution

  • As with previous versions, the installer for Scisoft OSX (due to bugs, apparently in Apple’s installer.app) changes the ownership of /Applications after the install. I would run Disk Utility and Fix the Permissions on your root volume after installing Scisoft OSX.
  • [Added Sept. 23] Gordon Richards and I have have been investigating some serious annoyances with the python installation on Snow Leopard in this version of SciSoft OSX.
    1. First of all, the installer apparently doesn’t install /Applications/scisoft/i386/Packages/Python-2.5.4/Python.framework/Versions/2.5/Resources/Python.app/ when running on Snow Leopard. This directory contains the python executable. Therefore, in the new SciSoft OSX on Snow Leopard, you can’t run python from the clean install. If you manually copy this directory from the previous SciSoft OSX installation to this one, then I find you can run python again (or in my case, pyraf). I can confirm this directory is apparently installed under Leopard.
    2. On Snow Leopard, Gordon Richards discovered that if you attempt ‘import pylab’ in python, you get a bus error. I can confirm the same error occurs on my Snow Leopard machine using either this SciSoft OSX release or the previous one. Furthermore, I can confirm the error DOES NOT occur in Leopard. I am not a heavy Python user, so I will leave it to Gordon, Nor, and others to investigate this issue. Gordon notes that this blog posting contains instructions for getting pylab installed under a vanilla Snow Leopard install, in case you need them.

The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.

Scisoft OSX 2009.6.1 Released 2

Posted on June 05, 2009 by admin

Nor Pirzkal has apparently been busy fixing the issues I noted in last month’s release of Scisoft OSX given his blog entry:

Scisoft OSX Intel 2009.6.1 Released

This version updates the STSDAS/TABLES packages and a few other packages.
It also fixes the issues pointed out by J. Cabanela

The new version of Scisoft OSX 2009.6.1 differs from Scisoft OSX 2009.5.2 in the following ways:

  • Stiff was updated from version 1.10 to version 1.12
  • HEASARC fv.app was updated from version 5.1 to version 5.2.1 and properly installed.
  • HEASARC hera.app was updated from version 5.1 to version 5.2.1 and properly installed.
  • HEASARC StudentHera.app was updated from version 5.1 to version 5.2.1 and properly installed.
  • SAOImage DS9 was updated to version 5.6.3 from version 5.3b.
  • Interestingly, the STSDAS and TABLES IRAF packages are still version 3.10, so I am not sure what updates Nor refers to above for STSDAS/TABLES.

The only glitch I noticed is that permissions problems persist. Specifically, when the installer installs Scisoft OSX, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:

sudo chown username:admin /Applications

(where “username” is the primary administrator’s username, in most cases, your username) to perform the repair. I know Nor spent a bit of time trying to resolve this without success last summer, so its a glitch that will probably persist.

I also have a minor gripe. This is not a bug, so much a feature I prefer. I like having the X11 command-line version of ds9 available, so I manually installed the current ds9 command line binary into /Applications/scisoft/i386/bin/.

The current version of Scisoft OSX is available for download from the Scisoft OSX website (or will be shortly) and I have made the package available on my Scisoft OSX mirror as well.

Scisoft OSX 2009.5.2 Released 0

Posted on May 15, 2009 by Juan

This first Scisoft OSX release of 2009 has appeared. Despite the brief entry on the VersionTracker website which said that this update rolled in the recently released STSDAS and TABLES IRAF package updates. from reviewing the CONTENTS file distributed with the install, I found Nor Pirzkal made quite a few additional updates in this release. The changes from Scisoft OSX 2008.9.1 are:

  • Eclipse 5.0.0 has been added to the distribution. Eclipse is an Integrated Development Environment (IDE) for programming. I don’t find it to be terribly useful, and in fact find it fairly awful in its implementation for IDL, but I am sure there are many people who disagree (enough to foster development of five major versions of it).
  • Gnuplot has been updated to version 4.2.5 from 4.2.3
  • Eye 1.4.1 has been added to the distribution. Eye is a program designed to allow you to use an artificial neural network to construct SExtractor filters for “adaptive filtering, feature detection and cosmetic corrections.”
  • Swarp was updated to 2.17.6 from 2.17.1
  • WeightWatcher was updated to 1.8.10 from 1.8.7
  • The Python distribution was updated to version 2.5.4 from 2.5.2 and the following python packages were updated:
    • ipython updated to 0.9.1 from 0.8.4
    • Numpy updated to 1.3 from 1.1.1
    • pyfits updated to 2.1.1 from 1.1 (or this could be a typo in the old CONTENTS)
    • matplotlib updated to 0.98.5.2 from 0.98.3
    • pyraf updated to 1.7.1 from 1.6
    • stsci_python updated to 2.8 from 2.6
    • AstroAsciiData updated to 1.1 from 1.0
    • scipy updated to 0.7.0 from 0.6.0
  • The STSDAS and TABLES IRAF packages were updated to version 3.10 from 3.08
  • fftw library version 3.2.1 added. This will be useful to me since we have been using fftw in the computational physics class I have been teaching this semester.
  • I noticed the Aquaterm.app application (used for graphics display by PGPLOT and Gnuplot) is now pre-installed in /Applications/scisoft/i386/Applications/.

Some minor glitches I have noticed in this distribution

  1. Permission Problems Persist: When the installer installs Scisoft OSX, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using: sudo chown username:admin /Applications (where “username” is the primary administrator’s username, in most cases, your username) to perform the repair. I know Nor spent a bit of time trying to resolve this without success last summer, so its a glitch that will probably persist.
  2. Older SAOImage DS9 included: I noticed that the SAOImage DS9 distributed with this version of Scisoft OSX is version 5.3b, whereas the current version is 5.6.1, so I manually installed the current ds9 command line binary into /Applications/scisoft/i386/bin/ and the current Aqua application into /Applications/scisoft/i386/Applications/ and everything is working fine there.
  3. HEASARC fv.app not installed: The fv.app application in the /Applications/scisoft/i386/Applications/ is actually a second copy of studenthera.app, misnamed. Not sure how that happened, but I manually installed the current version of HEASARC fv.app there without an issue.

All in all, a bunch of small updates, but it gets the package mostly up-to-date again. The current version of Scisoft OSX is available for download from the Scisoft OSX website, but I have made the package available on my Scisoft OSX mirror as well, in case it is faster for people.

SAOImage DS9 5.3 released (fixes Leopard Firewall issues) 0

Posted on October 15, 2008 by Juan

The folks at the SAO have finally released a version of SAOImage DS9 (version 5.3) that plays well with the current version of the MacOS Firewall (as of MacOS 10.5.5) . Here are the links to the downloadable Mac-related SAOImage files

To quote the release notes on the SAOImage DS9 website, the changes in the newly released version 5.3 are

Regions: Regions now support a centroid function. The centroid function can be manually invoked or regions can automatically snap to a centroid when moved or edited. Regions now have a DASH line property.

Colorbar: Now supports a vertical colorbar layout option, via the View Menu. Users can configure the font type and size of the colorbar, via the View Menu.

GUI: Now supports a vertical button bar, when in vertical layout mode.

Aqua MacOSX 10.5 firewall: The MacOSX Aqua 10.5 Leopard port of DS9 can be used with the MacOSX 10.5 firewall enabled.

X11 MacOSX 10.5: There are now two versions available for X11 MacOSX 10.5 Leopard. The non-firewall version is recommended for all unless you wish to enable the 10.5 firewall. [Juan’s Note: While not stating this, they mean specifically the application-specific version of the MacOS firewall. See my notes on this problem here.] In that case, please use the firewall enabled version. Please note: this version consist of 2 files, ds9 and ds9.zip. It is very important that ds9.zip be placed in the same directory as the ds9 binary at all times.

Contours: Contours now have a DASH line option.

I have previously posted notes for integrating upgrades of DS9 into the Scisoft OS X installation and they still work just fine except that newer releases of Scisoft OS X place the binaries in /Applications/scisoft/i386/bin/ instead of /scisoft/i386/bin/ and if you are installing the X11 binary that is compatible with the firewall, you have to install both the ds9 and ds9.zip file in the bin/ directory of Scisoft OSX.

Scisoft OSX Intel 2008.9.1 released 0

Posted on September 23, 2008 by Juan

Scisoft OSX Intel 2008.9.1 was released yesterday. Nor noted in his blog post about it that this is a bug fix release that

should resolve a few outstanding problems created when changing the location of scisoft from /scisoft to /Applications/scisoft/. Packages such as MIDAS and Gnuplot should now work properly.

This version removes some remaining dependencies on the HPC OSX compilers, which I had on my machine but which most users do not have (and do not want to have).

I compared the /Application/scisoft/i386/Packages directory from this release of Scisoft OSX to the last one and there are no new packages installed. The few issues I noted with the Scisoft OSX 2008.8.1 release all appear to still be valid. Notably:

  1. Permission Problems Persist: When the installer installs /Applications/scisoft, it appears that a bug in Apple’s Installer program triggers a change in ownership of the /Applications directory to that of the second user on the system. I strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:
    sudo chown username:admin /Applications
    

    (where “username” is the primary administrative users username, in most cases, your username) to perform the repair.
  2. ds9 command line executable missing: This release has the same glitch I noticed in version 2008.8.1 in that /Applications/scisoft/i386/bin doesn’t appear to have a ds9 binary installed. You can fix this by installing the X11 version of ds9 there or by linking to the Aqua version of ds9 that was installed using the command line
    ln -s "/Applications/scisoft/i386/Applications/SAOImage DS9.app/Contents/MacOS/ds9" /Applications/scisoft/i386/bin/ds9

I have placed a copy of this release in my Scisoft OSX Mirror in case the main Scisoft OSX repository gets bogged down.

Scisoft OSX 2008.8.1 released 1

Posted on August 27, 2008 by Juan

Scisoft OSX Intel 2008.8.1 was released about a week ago. I have been working with Nor Pirzkal for the last few months beta-testing this version and trying to make sure my concerns about the previous version were addressed. Nor’s blog post about the update states

There are a few changes in this version and all packages have been updated to the latest available versions. Starting with this version, Scisoft is installed in /Applications/scisoft (it previously was installed in /scisoft). Make sure that you remove any old /scisoft installation and properly update your startup files to source the Setup.csh or Setup.bash from their new locations.

In the README file you are told

Once the collection is successfully installed csh and tcsh users should invoke the command:

source /Applications/scisoft/all/bin/Setup.csh

to gain access to all the software and configure their environment correctly.

Users of the “bash” shell should instead use:

. /Applications/scisoft/all/bin/Setup.bash

Personally, to avoid problems in tcsh with a script breaking or with modifying my PATH multiple times by repeated execution of the Setup.csh script, I use the following line in my .tcshrc to first check for the existence of the Setup.csh script and SCISOFT environmental variables before executing it.

if (! $?SCISOFT) then
test -r /Applications/scisoft/all/bin/Setup.csh && source /Applications/scisoft/all/bin/Setup.csh
endif

Permission Problems Persist
This version addresses all the issues I noticed with Scisoft OSX 2008.5.1 except for one annoying one, the reassignment of ownership of the enclosing directory on installation. If you installed the old version of Scisoft OSX, it would reassign ownership of the root (/) directory to the second user on the system (in my case, since their is none, it showed the user as “502”). I beta-tested various versions of Scisoft OSX but Nor was not able to stamp out this particular problem. I believe Nor has come to the conclusion after extensive testing that this is a problem with Apple’s software for constructing installer packages. By moving the Scisoft OSX installation to /Applications/scisoft, it is the /Applications directory that gets its ownership changed instead of the root directory, which is less damaging. However, I would strongly suggest checking the ownership of the /Applications directory afterward and if isn’t owned by an administrative user, set it as such using:

sudo chown username:admin /Applications

(where “username” is the primary administrative users username, in most cases, your username) to perform the repair.

A Quick-Fix for any Legacy Scisoft-related scripts
If you had a few scripts that relied on Scisoft OSX being located in /scisoft and you don’t want to edit them all is you can make /scisoft point to /Applications/scisoft. This can be accomplished by first moving the old version of Scisoft OSX before installing 2008.8.1 via the command line:

sudo mv /scisoft /scisoft_old

and then once you have installed the new Scisoft OSX in 2008.8.1, create a symbolic link from the old location to the new by typing (again from the command line)

sudo ln -s /Applications/scisoft /scisoft

This will allow any scripts that refer to items in /scisoft to continue to work for the most part.

What’s New?
An investigation of the /Application/scisoft/i386/Packages directory as well as the NEWS file reveals the following changes to this version of SciSoft OSX over the 2008.5.1 version.

  • DS9 updated from 5.1 to 5.3beta
  • FV updated from 5.1 to 5.2.1
  • ATLAS updated to version 3.8.2
  • MIDAS updated to 08FEBpl1.1
  • cdsclient was updated to version 2.87
  • OpenMotif updated to 2.1.32_compat
  • cfitsio library updaed from 3.090 to 3.090 (the current version is 3.100)
  • pango library updated from version 1.20.2 to 1.21.3
  • pixman library updated from 0.10.0 to 0.11.2
  • expat library updated from 2.0.0 to 2.0.1
  • fontconfig library updated from 2.3.2 to 2.6.0
  • freetype library updated from 2.2.1 to 2.3.6
  • gettext library updated from 0.14.5 to 0.17
  • gtk+ updated from 2.12.9 to 2.12.10
  • libpng library updated from 1.2.10 to 1.2.29
  • netCDF library version 3.6.2 added
  • pkg-config updated from 0.20 to 0.23
  • TclTk package updated from 8.4.13 to 8.4.19
  • wcstools library updated from 3.6.4 to 3.7.3 (current version is 3.7.5)
  • IRAF package rvsao updated t version 2.5.7 to 2.6.4
  • Python was updated to 2.5.2 and the following Python libraries were updated:

Minor Glitches
The only other minor glitch I noticed was that /Applications/scisoft/i386/bin doesn’t appear to have a ds9 binary installed. You can fix this by installing the X11 version of ds9 there or by linking to the Aqua version of ds9 that was installed using the command line

ln -s "/Applications/scisoft/i386/Applications/SAOImage DS9.app/Contents/MacOS/ds9" /Applications/scisoft/i386/bin/ds9

Scisoft OSX mirror fixed 0

Posted on July 10, 2008 by Juan

When I moved the my Scisoft OSX mirror to a new server, I messed up the permissions on the files, preventing users from downloading the Scisoft OSX packages from the mirror. This has now been fixed.

SciSoft OSX 2008.5.1 Released (with my installation notes) 3

Posted on May 28, 2008 by Juan

SciSoft OSX Intel 2008.5.1 was released today. Nor’s blog post about the update states

The latest update to Scisoft OSX is now available. This includes an update to Pyraf (v. 1.6), GSL, pygsl, Gunplot, and a few backend libraries.

I went ahead and decided to install it today to investigate the improvements. As is usually my procedure, I first moved the directory containing my functional SciSoft OSX install temporarily out of the way via the command line:

sudo mv /scisoft /scisoft_old

Having done that I double-clicked on the installer package and let it do its thing, installing everything in the /scisoft directory. I poked around a bit an realized almost immediately that /scisoft/i386/Applications directory was empty! This one is kind of a show stopper as it means DS9 and FV are unavailable. I copied the files back from the previous installation without too much of a hitch. I did check, the installer package file with Pacifist and it does appear to contain those files in it, so I am not sure why they didn’t appear to install. I hope this is an isolated incident and not a recurring issue with the installer.

Other minor glitches I noticed:

  • I discovered that /scisoft/i386/Packages, /scisoft/NEWS and /scisoft/i386/share are set to have owner 502:502 instead of root:admin. This glitch is easily fixed by issuing the following command from the Terminal
    sudo chown -R root:admin /scisoft/
  • I also noticed that in addition to the x11iraf-1.5DEV installation, the entire x11iraf-1.3.2 installation is still sitting in the /scisoft/i386/Packages directory. All the x11iraf binaries in /scisoft/i386/bin/ are linked to x11iraf-1.5DEV instead of the older 1.3.2 binaries. I suspect this is an oversight.

An investigation of the /scisoft/i386/Packages directory as well as the NEWS file reveals the following changes to this version of SciSoft OSX over the 2008.3.1 version.

  • GSL updated from 1.9 to 1.11
  • DS9 updated from 4.13 to 5.1 (The current version of SAOImage DS9 is actually version 5.2, you can read about how to update the SciSoft version of DS9 in this post)
  • GNUPlot updated from 4.0.0 to 4.2.3
  • Swarp updated from version 2.15.7 to 2.17.1
  • WeightWatcher updated from version 1.7 to 1.8.7
  • pyraf updated from version 1.3 to version 1.6
  • The following Python libraries were updated:
    • pygtk updated from 2.8.6 to 2.12.1
    • matplotlib updated from 0.90 to 0.91.2
  • atk library updated from 1.10.3 to 1.22.0
  • cairo library updated from 1.1.6 to 1.6.4
  • cfitsio library updaed from 3.040 to 3.080
  • glib library updated from 2.8.6 to 2.16.3
  • glib-1.2.10 library added as well (possibly for a particular package needing older version of library)
  • gtk+ library updated from 2.8.19 to 2.12.9
  • gtk+-1.2.10 library added as well (possibly for a particular package needing older version of library)
  • pango library updated from version 1.10.4 to 1.20.2
  • pixman 0.10.0 library added
  • libtiff library upgraded from 3.7.4 to 3.8.2

Hats off to the SciSoft OSX folks for keeping this package up to date. I have placed a copy in my SciSoft OSX mirror in case there are any access issues.

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