Urania

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Archive for the ‘SciSoft OSX’


DS9 version 5.2 released 1

Posted on April 19, 2008 by Juan

[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:

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.

SciSoft OSX 2008.3.1 Installation Notes 3

Posted on April 06, 2008 by Juan
As noted in my last blog post, SciSoft OSX Intel 2008.3.1 was released a few days ago. While I am Cerro Tololo, last night was our “training night” on the instrument, so I did get a decent night of sleep, so I decided to take some time and see what is in this new SciSoft OSX Intel 2008.3.1 package in detail. Because I didn’t want to lose my functional version of SciSoft OSX, especially during an observing run, 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. 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,
      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:
      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.
      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 OSX Intel 2008.3.1 released 0

Posted on April 05, 2008 by Juan

I am Cerro Tololo preparing for our observing run starting tomorrow night with the Blanco 4-meter, so I don’t have much time right now to analyze the new version of Scisoft OSX that was released today, but it looks like they addressed quite a few of my comments from before about some of the Aqua applications being out of date. Here’s the release notes:

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.

Scisoft OSX 2008.2.1 (Intel only) released 3 weeks ago! 1

Posted on February 28, 2008 by Juan
It’s been such a busy month that I missed the fact that Nor Pirzkal has released a new version of SciSoft OSX. Released on February 4, 2008, this version, dubbed 2008.2.1 is only for Intel-based Macs. [1] This new version contains the following improvements:
  • Certain links to libraries that I have previously noted had to be manually fixed have been fixed.
  • The IRAF within SciSoft OSX has been updated to the latest release, version 2.14. However, as noted in his February 25 post, Nor notes if mkiraf fails to create a proper login.cl, you should do the following:
    edit /scisoft/all/packages/iraf/iraf/unix/hlib/mkiraf.csh
    and replace the first two uncommented lines with
    
    set iraf = "/scisoft/all/packages/iraf/iraf/"
    set imdir = "/scisoft//all/packages/iraf/imdirs"
I’ll update this blog post as I experiment with the new release. But just from looking at the release notes:
  • SAO Image DS9 is still at version 4.13 and not the current version 5.1. This is an issue mostly for Leopard users, since the older version of DS9 doesn’t run under Leopard without some tweaks. This is an easy enough upgrade.
  • fv (an interactive FITS file viewer) is still at version 4.4 instead of the current version 5.1. You can download the current version and replace the one in the /scisoft/i386/Applications directory in case you view this as necessary.
  • It installs /scisoft with permissions set such that the owner is the second user account created on most Macs (User 502). Previously it installed as owned by the first user account (user 501). This is not a huge issue if you have “sudo” privileges on the Mac (any “Administrative” user does, its the default on the first account created), just type the following on the command line:
    sudo chown -R root:admin /scisoft
    and enter your password when prompted. This will set the root account to own the files, which is appropriate in a multiuser situation. If you are the only user, you could set yourself up as owner by replacing ‘root’ above with your username (you can determine your username by typing “whoami” on the command line).
I have placed a mirror of this new version on my Unofficial Scisoft OSX Mirror page as well
Linknotes:
  1. Why No Current PPC Version of SciSoft OSX – I suspect the reason all the recent releases have been Intel-only is because it isn’t a simple matter to recompile these programs for PowerPC. These packages were designed for unix-based environments and are NOT Mac-specific. So they were not built using Apple Xcode [in which case building a ‘universal’ application is just an option in the compiler] but instead using the command line based make command. This means getting an intel-native binary involves hacking a Makefile for each package. And given the byte endianness differences between intel and PowerPC chips and the number of tweaks this would entail in the various makefiles used to build SciSoft, I understand completely why these releases are intel-only.

SAOImage DS9 5.1 released 2

Posted on January 14, 2008 by Juan

The folks behind SAOImage DS9 have now released version 5.1. The big change I’ve noticed since the last version is that version 5.1 works without issues under Leopard’s new X11 implementation. Of course, the disadvantage is you now must download a version compatible with your OS version as well as your CPU.

More detailed release notes are available here. See my previous post on SAOImage DS9 5.0 to see how it is possible to upgrade the binaries included with SciSoft OSX.

Scisoft OSX Unofficial Mirror Site 0

Posted on December 24, 2007 by Juan

Because a reader of this blog contacted me to inform me that the official Scisoft OSX download links appear to be down (scisoftosx.dyndns.org is not resolving), I have placed a mirror of the latest versions for both PPC and MacIntel online here. I will take down this mirror if the maintainers of Scisoft OSX ask, but at least for now, it is online.

Scisoft OSX 2007.11.2b Notes 2

Posted on November 16, 2007 by Juan

No… the new Scisoft OSX isn’t out quite yet, but I got the following note from Nor Pirzkal responding to my post regarding the various broken symbolic links in SciSoft OSX 2007.11.1.

Just to let you know that I just implemented your changes in 2007.11.2b. Thanks again.

So it looks like these bugs will be fixed when Scisoft OSX 2007.11.2b is released soon. I have to hand it to them, Nor is pretty quick to respond to these bugs, given he has a full time job which doesn’t involve maintaining SciSoft OSX!

Scisoft OSX 2007.11.1 Released 2

Posted on November 01, 2007 by Juan
Wow, Nor Pirzkal and Francesco Pierfederici have kept quite busy making small updates to Scisoft OSX for Intel. They released another new version today (available for download here). Here’s the entire description of the changes in this version of Scisoft OSX from the release notes:
This version updated Python to version 2.5.1 and correct some minor issue with the bash version of the irafuser.bash script when running under OSX 10.5 Leopard. Missing GCC runtime fortran libraries are also now included. This version was test under OSX 10.5 and seems to run fine. Note that 10.5 does deal with X11 applications slightly differently. Once the Setup.bash script has been source[d], you should add the following line to your .bash_profile: export DISPLAY=127.0.0.1:0.0 This will enable all Scisoft X11 applications to start from Terminal.app
I am not running Leopard (and probably will not switch until the winter break, when I have time to deal with all the X11 issues it creates), so I can’t confirm the ability to run under Leopard, but its great to know they are keeping SciSoft OS X up to date.

Issues with this Release of Scisoft OSX
  • I did notice this new version of Scisoft OSX doesn’t appear to link its IRAF install with the rvsao IRAF package (used for radial velocity computations). Doesn’t matter to me to much since I compiled the newer version and linked to it, but it is funny they include the rvsao package at /scisoft/all/packages/iraf/extern/rvsao but don’t link to it in the $hlib/extern.pkg file, which I do believe they did in the older versions.
  • I may not have noticed this earlier, but in the libraries directory /scisoft/i386/lib, some of the symbolic links are broken. Specifically:
    • All the items in this directory linking to the OpenMotif library items are not linked, it appears /scisoft/i386/Packages/OpenMotif-2.3.0/lib doesn’t exist. However, /scisoft/i386/Packages/OpenMotif-2.3.0/lib.org does. So I symbolically linked lib to lib.org via:
      cd /scisoft/i386/Packages/OpenMotif-2.3.0/
      ln -s lib.org/ lib
      And now all the links to the OpenMotif libraries within /scisoft/i386/lib work.
    • The CFITSIO library is mis-linked to an older version which no longer is installed. So I needed to:
      cd /scisoft/i386/lib/
      rm libcfitsio.a
      ln -s ../Packages/cfitsio-3.040/lib/libcfitsio.a libcfitsio.a
      and the CFITSIO library was properly linked again.
    • libpng.so was apparently not compiled within /scisoft/i386/Packages/libpng-1.2.10/lib, so there is no quick fix for that broken link.
    • I removed a link to python2.4 in /scisoft/i386/lib and replaced it with a link to python 2.5:
      cd /scisoft/i386/lib/
      rm python2.4
      ln -s ../Packages/pygtk-2.8.6/lib/python2.5/ python2.5
  • All the CFITSIO headers in /scisoft/i386/include/ are linking to an older version (3.006) instead of the current installed version (3.040). Fixed via:
    cd /scisoft/i386/include/
    rm -f drvrsmem.h fitsio.h fitsio2.h longnam.h
    ln -s ../Packages/cfitsio-3.040/include/*.h .
  • There are symbolic links in the /scisoft/i386/bin directory to a variety of executables from the sm plotting package which doesn’t appear to have been installed as part of the Scisoft OSX distribution.
  • Not really a bug, but the version of SAOImage DS9 is version 4.1.3 and not the current version 5.0.0. Of course, given the long history of dangerous version X.0.0 software, this maybe safer that way.

SAOImage ds9 version 5.0 released 1

Posted on October 16, 2007 by Juan
On October 15, the folks behind SAOImage released SAOImage DS9 version 5.0. The big change I noticed is they now have a completely MacOS X native (read “Aqua”) version of ds9 (but only if you use the application package version of ds9, the command line versions remain X11)! I downloaded the following three versions: The new features lists page tells us that this release includes:
  • MacOSX Aqua Support: DS9 has been ported to MacOSX Aqua and is an universal application which no longer requires X11.
  • Compressed FITS Support: DS9 supports compressed FITS images using RICE compression.
  • Mask Support: DS9 supports overlay masks. A mask is defined as a valid FITS image, in which a non zero value indicates that the selected mask color is to be displayed instead of the data value color.
  • SkyView Support: DS9 provides support for HEASARC’s image cutout service, SkyView. This site provides image cutout service for a number of image surveys, including SDSS.
  • Multi-Language Support: DS9 provides multi-language support. By default, the language used for menus and dialog boxes is based on the value of the operating system locale variable. The user may override the default value by selecting the desired language in the preferences or by the -language command line option.
  • Preferences: Preferences are automatically saved when a user changes an option. Selecting the saving preferences menu item is no longer needed.
More detailed release notes are available here. I was able to get this version of ds9 integrated with SciSoft OSX by doing the following:
  1. Decompress the command line version of ds9 via the terminal using tar xzvf ds9.darwinppc.5.0.tar.gz (PPC version) or tar xzvf ds9.darwinintel.5.0.tar.gz (Intel version). When the decompression is done, all you have is an executable called ds9.
  2. Next, from the terminal, go to the /scisoft/bin directory (on PPC) or /scisoft/i386/bin/ directory (on Intel) and rename the old ds9 executable to something like ds9_old (using something like mv ds9 ds9_old).
  3. Copy your newly decompressed ds9 executable into the SciSoft OSX binary directory. I should note the command line version of ds9 still requires X11.

Scisoft OSX Intel 2007.9.1 released 0

Posted on September 18, 2007 by Juan

Another new version of Scisoft OSX for Intel has been released and is available for download here. Here’s the entire description of the changes in this version of Scisoft OSX from the release notes:

This version contains an updated [ESO-]MIDAS package.         

I checked the list of packages included and sure enough, the only change was in the ESO-MIDAS package (whose current version is actually 07SEPpl1.0).

I don’t use ESO-MIDAS, which is an image reduction package aimed as users of ESO’s La Silla facilities and the VLT at Paranal, so I can’t really comment as to the usefulness of this update. As with previous versions of Scisoft, the release notes warn if you use Aquaterm devices for PGPLOT, GNUPLOT, or any other packages that you “must manually run /scisoft/i386/Applications/Aquaterm.app once first to enable the aquaterm devices.”

I have also confirmed that this release also fixes the IRAF problem with symbolic linking to mkpkg and xc in /scisoft/i386/bin/ I referred to earlier in my blog.   Thanks for the fix guys!

Finally, as I noted with the last release of Scisoft, my standard method for updating Scisoft OSX is to move my existing /scisoft directory to /scisoft_old and then I unpack the new version. That way, in case anything goes wrong, I can always switch back.

Annoyance: IRAF in Scisoft OSX mkpkg glitches 1

Posted on August 08, 2007 by Juan

Update: I have updated this blog entry to reflect some updated information from Nor Pirzkal regarding the best way to fix this glitch.  This problem has been fixed in Scisoft OSX MacIntel version (2007.9.1).

During my adventures compiling the hectospec-related IRAF packages, I was using Scisoft OSX and discovered there were a couple of issues with the symbolic links for the mkpkg command necessary for compiling new IRAF packages.

  • In the Scisoft OSX PPC Beta (2006.11.1b) mkpkg appears to be mis-linked, so it can’t be executed. So I did the following in the terminal:
    cd /scisoft/binsudo rm mkpkgsudo ln -s ../iraf/iraf/unix/bin.macosx/mkpkg.e mkpkg
  • In the Scisoft OSX MacIntel version (2007.1.1) and Scisoft OSX MacIntel version (2007.7.1), there are some missing symbolic links to mkpkg and xc in the directory for MacIntel binaries.  As a result, both mkpkg and xc were instead pointing to PowerPC binaries. I fixed this as follows (again, from the command line):
    cd /scisoft/i386/bin/sudo ln -s /scisoft/all/packages/iraf/iraf/unix/bin.macintel/mkpkg.e mkpkgsudo ln -s /scisoft/all/packages/iraf/iraf/unix/bin.macintel/xc.e xc
    This mis-linking certainly didn’t help getting things to compile under MacIntel, since IRAF was attempting to compile MacIntel code using PowerPC versions of mkpkg and xc.

Thanks for Nor Pirzkal for giving me some feedback on fixing this problem.  He tells me he has made the appropriate changes so that the next version of Scisoft OSX will not have this  issue.By the way, my complaint here should in no way be construed as a critique of the efforts of Francesco Pierfedericki and Nor Pirzkal in putting together Scisoft OSX. They have done a great deal of work to put together an awesome package. For two people to track over 2 GB of software and not expect some glitches is unrealistic. And I for one am extremely grateful that his efforts have saved me a lot of time.

HINT: Maple from the Command Line 0

Posted on July 18, 2007 by Juan

Maple is a nice symbolic mathematics pages from the Canadians at Maplesoft. Our school as a site license which is an awesome deal as students can buy personal copies for much less than the price of a typical textbook. As such, our students can be expected to use the software for their classes. One of the really slick bits on the Mac is you can run Maple from the command line (useful when I need to compute an integral quickly).

I am running Maple 11, so I just placed the following alias in my ~/.tcshrc file (I run tcsh by default because I am old school and dislike bash):

alias maple "/Library/Frameworks/Maple.framework/Versions/11/bin/maple"

If you are running the PPC version of SciSoft, it messes around with some environmental variables, breaking this trick, you can instead use
alias maple "unsetenv DYLD_FALLBACK_LIBRARY_PATH; /Library/Frameworks/Maple.framework/Versions/11/bin/maple; setenv DYLD_FALLBACK_LIBRARY_PATH /scisoft/lib"

If you are using Maple 10, substitute a “10” where you see an “11” above.

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