Urania

I can attest the Aqua version of SAOImage DS9 version 5.3beta does indeed play nice with Apple’s dopey firewall behavior (see here for notes on version 5.2’s incompatibility with the Leopard firewall). However, the command line version that uses X-windows DOES NOT play nice with the Leopard Firewall. If you run the X-windows version of “ds9″ on a Mac running Leopard’s built in Firewall in “Set access for specific services and applications”, you will end up with a completely hosed ds9 executable which will not launch ever again.

As such, for now, since I prefer the X-windows version of SAOImage DS9, I am leaving the the Firewall off for now, I’m not too concerned.

Today I noticeed two interesting software updates for Mac-based professional astronomers.

The first one I noticed was the updating of Xquartz to version 2.3.0. Xquartz is the updated version of X11 for the Mac OS (even ahead of Apple’s own installed versions) that I prefer to use, largely because bug-fixes get rolled in here before they appear in Mac OS. This version requires Mac OS 10.5.4 and has a couple of caveats attached to it for programmers, notably:

The software supporting the deprecated imake build system is not provided in this package. If you need imake and xmkmf, please install the X11 package that came with your Leopard DVD before installing this version. Alternatively, you can compile these packages on your own or get them from a third party such as Fink or MacPorts. The darwin configuration files used by the imake build system are outdated and not supported. Developers using this build system are advised to migrate to autoconf.

[Added July 24, 2008: Apparently, this version of Xquartz changed the X11.app Icon so it now X11 looks like this

when it is on the Dock. Interesting, but it threw me for a second. The only documentation I found of this change is in a Ticket filed with XQuartz's bug reporting system. Still, I think this is a good idea, as it gives a visual cue that you are using XQuartz as opposed to the default X11 installation.]

Along with a bunch of library changes, the key update appears to be having the Xserver updated to the 1.4 branch of Xorg. There is also “support for adding new $DISPLAY sockets after the server is running” (which I think means using the DISPLAY variable will not break things) and “/usr/X11/bin/Xquartz is just a stub that will ‘do the right thing’,” whatever that means. I have upgraded to it and as a reminder, if you upgrade MacOS after installing Xquartz, you will need to reinstall Xquartz to get it back.

The other interesting software release for Mac-based astronomers I noticed today was SAOImage DS9 which has released version 5.3beta, which appears to be, based on the statement on their homepage that “MacOSX 10.5 users with firewall enabled, please use version 5.3 beta”, geared toward addressing the issue I noticed this April with version 5.2 where launching SAOimage DS9 with a certain firewall setting on the Mac could result in the the application becoming irreparably damaged at launch.

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.

I was trying to upgrade wine within MacPorts when I realized I had forgotten to upgrade Xquartz after my upgrade to MacOS 10.5.3 on my Mac Pro. So I checked, Xquartz has been upgraded to version 2.2.3. Since version 2.2.1 (which I talked about in my blog here).

• 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).

I have been an avid Firefox user for quite some time. But when I moved to Intel-based Macs, I discovered that that Schubert’s PDF Browser Plugin didn’t work on Intel Macs (except if I placed Firefox in Rosetta mode, running its PPC code in emulation). hat project appears to have died on the vine, with no updates in abut 2 years. Furthermore, Adobe has insisted on making its inline PDF plugin Safari-only. This always struck me as rather redundant, since Apple has used Mac OS X’s Quartz graphics engine to allow viewing of PDFs inline in Safari. This, combined with Firefox’s longer launch times, made me slowly shift to using Safari about 80% of the time.

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

We had a set of hard storms come through yesterday afternoon. I was doing SkyWarn spotting with the local hams. I think (but will leave it to experts to confirm) that the structure under the smooth part of the storm (”the shelf) is a wall cloud. For a sense of scale, this is 8 photos stitched together covering above a fifth of my horizon and the leading edge of this storm when it was about five miles away.. Shortly after I shot this picture, the sirens went off. Rotation was spotted, but luckily, no funnel cloud touched down. Thankfully, while the storm blew through at 60 miles per hour, we had no significant damage… Still, it looked mean…

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.

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.

The Xquartz project is a useful one for Leopard users of astronomical applications because of the dependence of most astronomical applications on X11. A few days ago (what can I say, its finals and I am swamped with exam writing and grading) they released version 2.2.1. It contains all the tweaks that made it into the previous version and also includes

• 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 was posted on my friend John Martin’s blog. He is an astronomer and an educator, like myself. As finals roll around and students realize that slacking off in the class is going to have consequences, they get… creative. Here is John’s post:

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]

Immediately after installing SAOImage DS9 5.2, I had a major failure of the application and initially I just thought it was some sort of build bug. This is what I posted at that time:

[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!

[See my more recent post warning about MacOS X Firewall settings and how they can destroy the SAOImage DS9 executable during its first launch! This problem is avoidable by tweaking the Firewall settings, but once you have launched SAOImage DS9 with the bad settings, the application is damaged can can't be relaunched again. A reinstallation is the only solution, so it is a good idea to avoid this problem.]

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.

One of my favorite little programs is LaTeXit.  It allows you to typeset LaTeX equations outside of a text editor and then drag the results into programs like Keynote or Pages.  It was not fully compatible with Leopard and my fix was a kludge that could break other programs.  Pierre Chatelier has released updated LaTeXit to version 1.15.0, which restores Leopard compatibility.  Notably, you can now use the default0 /etc/profile file without fear.