• Upgraded the freetype library to version 2.3.6, which fixes “A bunch of potential security problems have been found [and fixed in this release”
• Upgraded to pixman library to version 0.11.4.
• Xquartz fixes from xorg-server-1.3.0-apple21, the key fix being support for monitor hotplugging, although several security fixes also occurred.

Again, if you upgrade MacOS (say to version 10.5.4, which is supposed to be released soon in order to support iPhone G3 and MobileMe), you will likely need to reinstall Xquartz (unless Apple has upgraded their X11 installation to match Xquartz).

Yesterday, Firefox 3 was released. I have been using the betas for the last month and have been happy with its improved speed and functionality. Its part of the reason I am back to about a 50/50 split in Safari vs. Firefox use. Today, the other show fell in the form of this posting on MacOS X Hints:

There is now a Firefox extension named firefox-mac-pdf, available for Firefox 3 under OS 10.5 that utilizes the built-in PDF support in OS X to display PDFs in-browser. In my testing, it appears to work very well. It doesn’t have the nifty fading bezel that the Safari PDF viewer does, but it supports all the same keyboard shortcuts and you get the standard Mac OS PDF contextual menu when you control-click on a displayed PDF.

Its interface is not quite as easy to use as Schubert’s plugin, but it works. I now have inline PDF viewing in Firefox and things are better in the world again.

Saving PDFs: The one issue I noticed is there was no seemingly obvious way to save the PDF once you were viewing it. Nothing in the contextual menu allowing “Save as…” for example. Turns out it was easier to save the PDF than I imagined. In the “Issues” page for firefox-max-pdf I found this exchange which included the solution:

Currently there are two ways of saving the PDF:

1. File->Save Page As menu
2. The apple-s (command-s) keyboard shortcut

Addendum: I sent the picture to Greg Gust, who runs some of the SkyWarn stuff for the National Weather Service in Grand Forks. He sent me these additional comments:

Most of the structure is a classic shelf cloud on the leading edge of a line of thunderstorms… this the widespread strong to severe winds as it came through. One the south end was the feature that we believe was a wall cloud… rotating updraft… and was what prompted us to issue the Tornado Warning across the southern part of Fargo and Moorhead.

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
  

  <br />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.

• All packages updated to versions intended to ship as part of X11R7.4 (as of 2008.04.21).
• Fixed multiple crash-causing bugs in the server.
• Fixed cmd-tab to properly move all windows forward when entering X11.app.
• Cleaned up multi-monitor support (still not completely bulletproof) [I have 2 monitors, so this is a big one for me].

As I have noted before, Apple includes some of the work done in this project in OSX updates, so it is suggested that you install the latest XQuartz release after updating to 10.5.2 (and any future 10.5.x or security updates).

This warning should be posted under my class in the course offering directory:

WARNING The Astronomy-Physics program has determined that doing poorly in Astronomy 101 may have deleterious impact beyond your GPA. Students failing Astronomy 101 report a higher incidence of: deaths of grandparents, close relatives who discover they have cancer, chronic personal health problems, influenza outbreak, computer hardware failure, traffic accidents, complete melt down of their university email account, death of beloved pets, and inability to find adequate child-care services. A high degree of correlation has been observed, however the cause-effect relationship is still under study. Students should be advised to enroll in this course and take it lightly at their own risk.

[From Warning About Doing Poorly in Astronomy Class]

[HOLD OFF ON THIS UPDATE! I have discovered that at least on one of my systems, this version of ds9 is refusing to run properly. It launched once, but when I attempted to check the “About SAOImage DS9”, it triggered the following error:

 “An internal error has been detected local header mismatch couldn't open “zvfsmntpt/doc/sun.gif”: no such file.

(this occurred in both Aqua and X11 versions). Furthermore, all future attempts to launch ds9 (again, either Aqua or X11) fail with the following error:

Error in startup script: couldn't read file “./zvfsmntpt/src/ds9.tcl”: no such file or directory  

Even removing the preferences file at ~/.ds9.prf didn’t help.]

Apparently, my problems with SAOImage DS9 in Leopard are a known issue. If you configure the built-in Firewall to “Set access for specific services and applications” so that you can approve “holes” in your firewall on an Application by Application basis, your first launch of SAOImage DS9 will irreparably damage the application!  Unfortunately, Apple implements the application firewall in part by modifying the Application package of the Application you are running by digitally signing it if it was not digitally signed by the developer (adding a file called CodeResources to the Application package). According the Apple’s documentation on this:

If you run an unsigned application not in the Application Firewall list, you will be presented with a dialog with options to Allow or Deny connections for the application. If you choose Allow, Mac OS X 10.5 will sign the application and automatically add it to the Application Firewall list. If you choose Deny, Mac OS X 10.5 will sign the application, automatically add it to the Application Firewall list and deny the connection.

So basically,Apple doesn’t warn you in the dialog box that comes up that it has whatever decision you make, it will modify the application by digitally signing it and it doesn’t give you a way to avoid this. This is, in my opinion, is an incredibly boneheaded move on Apple’s programmer’s part. They readily admit that

  Some applications check their own integrity when they are run without using code signing.

They suggest the application firewall will try to automatically detect these and avoid modifying them, but they should give you, the user, the option instead of making the decision via some internal algorithm.  MacOS X shouldn’t assume its OK to change an application. In the case of SAOImage DS9, they are irreparably damaging the application without leaving you a way to avoid the damage once you trigger the application firewall. Shame on you Apple. The only way to fix it is to reinstall the application!

So when I figured this out (a tip of the hat to this post on IRAF.net). I reinstalled the SAOImage DS9 executables (both Aqua and X11 versions) and before launching them, I set the Firewall (via the Security Pane of the System Preferences) to “Allow all incoming connections” (this is the default mode, so it is as secure as MacOS Tiger was). Everything now appears to work just fine.

Personally, I believe an application that fails its checksum should present a message indicating that is the problem instead of just crapping out, but in this case, the fault lies mostly with Apple. Apple is damaging applications by making this critical decision in the background, without user intervention!

The folks in Cambridge have kept busy. They have released SAOImage DS9 version 5.2. The versions for MacOS X include the following:

• Aqua 10.4 Tiger (Universal)
• Aqua 10.5 Leopard (Universal)
• X11 10.4 Tiger (Universal)
• X11 10.5 Leopard (Universal)

The rather extensive changes are detailed in the release notes here, but the notable ones to me include:

• ANALYSIS: for MacOSX tiger, wrap cmds with shell and PATH.
• GUI: change default directory for standard dialog to $HOME.
• ANALYSIS: add /sw/bin to default path for MacOSX. While unstated in the release notes, this is clearly an attempt to support Fink, which places its installation in the /sw directory.
• GUI: ds9 will now start in the users home directory for MacOSX Aqua users when invoked from a double click and the default dialog box is Motif or Windows.
• MACOSX: fixed a problem with printing non standard colors.
• MACOSX: restore postscript printing.
• REGIONS: apply WCS to fits regions if present.
• GUI: add support for user configured button bar.
• CATALOGS: add support for simbad.
• IMEXAMINE: added support for key stroke events.
• Although unstated in their release notes, they are now apparently providing universal binaries instead of PPC and Intel binaries for MacOS X.

I have previously posted notes for integrating upgrades of DS9 into the Scisoft OS X installation and they still work just fine.

Above Photo is the fox with the Blanco 4-meter telescope in the background.

The Above Photos show the first first nibbling on something than turning around, apparently looking at the small telescopes on the Cerro Tololo summit.

Funny thing is as I was dumping the pictures from my camera, Roberta knocked on my door, and I opened it, just in time to see one of the foxes run behind Roberta in my field a view. I pointed it out to her and she was happy the foxes were not completely gone.

The Xquartz folks have updated Xquartz to version 2.2.0.1. Xquartz is an effort to provide a better X11 server for Leopard than Apple provides, being proactive in providing fixes Apple will likely include later. The release notes are long and cover a bunch of updates to various items, including:

• Added informational output when falling through to failsafe startup in X11.app
• Unsetenv(DISPLAY) when falling through to failsafe startup in X11.app
• Exposé now works as expected
• X11 works better with spaces

I suspect the discussion of ‘failsafe’ startups is to provide a more informational failure than what was happening before for people like myself who transitioned from previous MacOS X installations and had been manually forcing the DISPLAY variable to point to :0.0, which is somewhat standard in the Unix world.

I’d recommend grabbing this Xquartz update and applying it if you use Leopard and astronomical software. Its a double-click install. Apple does watch this project (one of the developers is Apple’s X11 developer), and as noted on the Xquartz site:

Apple included some of the work done in this project in their 10.5.2 update and will likely include further changes in possible future updates of 10.5.x. It is suggested that you install the latest XQuartz release after updating to 10.5.2 (and any future 10.5.x or security updates).

In other words, while some of these fixes will likely end up in the official MacOS released by Apple, if you want them now, use Xquartz. Furthermore, since Xquartz does over-write Apple’s default X11 install, this means that if Apple upgrades X11 in a future patch, you could end up with a broken install if you used Xquartz. Personally, I haven’t had a problem, but I suggest you keep the Xquartz package around, and re-install it after any future MacOS X updates.

It will take us a good chunk of the summer to know what the results of this run actually are, such is the nature of astronomical data, but all in all, this feels like it has been a very productive run. In addition to the “science objectives” of this trip,  I have seen some of the darkest skies imaginable.  Since my interest in astronomy started by my attempts as a 6 to 7 year old to understand our place in the vastness of that sky, it has also been somewhat fulfilling to the soul to see the Universe in this way, the way humans saw it before the advent of artificial lighting.  Call this Chicken Soup for the Astronomer’s Soul.

That said, I am now ready to go back home to my family who I miss and my students whom I have to guide to finals. Just a few more hours, another short 5 hours of sleep, than I take the carryall to La Serena. Dr. Humphreys, my collaborator, will give a talk there tomorrow afternoon. We’ll do dinner afterward, and then tomorrow, I start the 24 hours of flights and connections it will take to get me home.

sudo port -d selfupdate
sudo port -d sync
sudo port install osxutils 

Since each exposure is 10 seconds, in some frames you see ‘lines’ appear, these are typically airplanes or possibly satellites.

The bright “star” to the East (left) of the Galactic Center in the last few frames is the planet Jupiter. Also in the last few frames you start seeing a glow in the eastern sky, almost pointing toward Jupiter. This is the Zodiacal light, sunlight reflecting off dust particles in the plane of the solar system. You need quite dark skies to see that.

I realize how dark the skies are here every time I go outside now. The Center of the Milky Way is passing overhead and it just screams out at you to be noticed. You can see it clearly on the right side of this picture, shot by Roger Smith of NOAO/AURA/NSF. It shows the 4-meter at Cerro Tololo shot at night. This is what the skies look like here. Admittedly this picture goes a bit deeper than human vision, but I would swear it isn’t much deeper. At home, we can’t see the Milky Way easily, even 15 miles from town, because of the light pollution and the fact that the Galactic Center is very far south. Here, you can’t avoid it! The Large and Small Magellanic Clouds, two irregular galaxies orbiting the Milky Way, are clearly visible to the human eye (they are on the right side of this picture).

And just a few minutes ago I saw something I have never seen before, Zodiacal Light. I am seeing sunlight reflecting off dust grains in the plane of the Solar System. Something only possible because of these extremely dark skies. Cool!

Tonight is starting off better. The clouds dispersed (mostly). The autoguider is working. And while we lost about 45 minutes to fiber issues, it looks like those may be vanquished as well. Hopefully the telescope gremlins that were working against us last night will be gone tonight. We are on our first 50 minute exposure, so I am going to bang out this post quickly.

Here’s some more pictures I have taken around here during the few hours of daytime I have been awake.

This is the telescope we are using, the 4-meter Blanco telescope on Cerro Tololo. This is a stitched image composed of 6 single frames. Because I was relatively close to the telescope, there is a distortion here similar to a fisheye lens image. To get a sense of scale, notice the double doors to the lower right hand side of the telescope itself.

This is an image of the other telescopes on the peak of Cerro Tololo shot from the catwalk around the 4-meter. From left to right the larger domes contain the 60-inch (1.5 meter), 36-inch (0.9 meter), the Yale 1-meter (which I used in April 2006), and the Michigan Schmidt Telescope. There are a few smaller telescopes in the background. About 50 miles behind the telescopes is the La Silla observatory (not visible in this picture).

There were some clouds here earlier today. This is the view from the peak of Cerro Tololo towards Cerro Pachon, which the rightmost mountain in this image. On its peak you can see (as small dots in the thumbnail) the SOAR telescope on the left and the large Gemini South 8-meter telescope on the right. I love the clouds in the background rolling over clouds, towards Argentina.

This is another 180 degree panorama shot from a bit up the hill from the dormitories. It shows Cerro Tololo on the right and on the left, appearing more distant than it really is, Cerro Pachon. If you squint, you might see the Gemini South 8-meter in this image.

Finally, another 180 degree panorama of the western horizon as seen from my dorm room right around sunset tonight. Those pink clouds, illuminated by the setting sun, are over Argentina. They form over those mountains to the west of us, Cerro Tololo rarely sees puffy clouds like those, it rarely sees clouds (except in the winter), and when it does see clouds, they are high cirrus as shown in the picture above.

Here’s a version of the image with some of the features/telescopes labeled (yes, I misspelled dormitories in the image, its not worth fixing it right now).

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. According the CONTENTS file at the top level of the /scisoft directory, the main changes were

• If you have SuperMongo (SM), you can request the new version. It has jumped from version SM 2.4.16 to SM 2.4.26. I don’t have a license for SuperMongo, so I can’t report much beyond this. This version of SM has Aquaterm support.
  
  
• FV, the FITS file viewer, was updated to version 5.1 from version 4.4 (they changed numbering conventions, I think). The CONTENTS file accidentally lists it as version 1.1.
  
  
• Numpy (which is used in PyRAF extensively) was updated from version 1.0.3 to the current version 1.0.4.
  
  
• stsci_python (which is also used in PyRAF extensively) went from version 2.5 to the current version 2.6.
  
  
• The mkiraf command line program that creates user’s IRAF directories appears to have been fixed for c-shell users. The bug (along with a fix) had been noted by Nor Pirzkal on his blog, so I am not surprised it was rolled into this release.
  
  
• The IRAF external packages STSDAS and TABLES when from version 3.7 to current version 3.8. The change in STSDAS includes a new package for processing WFC3 data (since I don’t use HST, I’m not that excited at the moment by this change, but I am sure someone is).
  
  
• The ESO-MIDAS version is listed as unchanged from the last release of SciSoft OSX, although the release notes just noted that “[t]his version includes a recompiled version of MIDAS (which was not tested under 10.4)”. The installed version is listed as 07FEBpl1.1 whereas the current version is 08FEBpl1.1.
  
  
• The version of DS9 included with this install of SciSoft is the current version 5.1 Aqua. This replaces the X11-based version previously included. I haven’t checked to see if it works in previous MacOS X installs, but it works fine in MacOS 10.5.2 (aka Leopard). If you do need to install a version of ds9 more appropriate to your MacOS X or if you are like me and prefer the X11 version of ds9, you can easily change the installed version.
  
  • If you are using an earlier MacOS X than Leopard and find the Aqua version of DS9 isn’t working, you can download an appropriate DS9 for you at http://hea-www.harvard.edu/RD/ds9/ and install it within SciSoft by noting that SciSoft OSX places the DS9 application at /scisoft/i386/Applications/SAOImage DS9.app. You could rename the installed DS9 application via the Finder or from the command line,
    

    <br />mv /scisoft/i386/Applications/SAOImage DS9.app /scisoft/i386/Applications/SAOImage DS9 (Disabled).app
    

    then if you want the Tiger (Aqua) version there, just place it in the /scisoft/i386/Applications/ directory.
    
  • I happen to prefer the X11 version of DS9 usually because I use pipe files to connect my IRAF session to my DS9 session and I have found that the Aqua version of ds9 doesn’t seem to play nicely in this regard. Its for that reason I installed the X11 version over the command line ds9. To do this, I noticed the command line ds9 is at /scisoft/i386/bin/ds9 and is just a symbolic link to the ds9 binary within the Application. You can just rename this symbolic link at /scisoft/i386/bin/ds9 from the command line:
    

    <br />mv /scisoft/i386/bin/ds9 /scisoft/i386/bin/ds9.old
    

    and place the executable ds9 file that is in the X11-version tarball of ds9 there instead.

    <br />mv ds9 /scisoft/i386/bin/ds9
    

    This has the added advantage of leaving the Aqua version of DS9 completely intact.
    
  
  
  
• I noticed this version of SciSoft OSX does install with me as the owner (instead of user 502). I don’t know if that is because it is defaulting to user 501 or because a change occurred in the SciSoft OSX installer, but its a welcome change.

That’s it for what I have noticed for now. This update addressed all of the issues I has noted with the previous version. Thanks guys!

One very mild issue I have with this version of SciSoft OSX. I noticed the RVSAO external package for IRAF included with this version of SciSoft OSX is Version 2.5.7. That’s several versions older than the current version. Its easy enough to install the current version in another directory (I use /usr/local/iraf) and then edit the /scisoft/all/packages/iraf/iraf/unix/hlib/extern.pkg file to point to the newer install, but I thought I would note that.

Scisoft Intel 2008.3.1 is available. This version includes a recompiled version of MIDAS (which was not tested under 10.4), updates to STSDAS/TABLES and a few other packages such as FV, STScI_Python, and DS9 Aqua.

I’ve placed a copy Scisoft OSX Intel 2008.3.1 on the online mirror, but I will also keep last few versions around for a while until I can evaluate this one. I suspect users may this version of SciSoft OSX may have issues running under 10.4, given the comment above in the release notes. I believe if you install DS9 yourself, you have to install the version specific to your MacOS version.