Archive for the 'Other Software' Category
Update at the bottom
According to commenter Erin, the Spot and Leopard tools from Spitzer don’t work on OS X 10.5 due to a Java issue. I haven’t tested this myself but I’ll try to verify this evening when I’m back on a Mac running Leopard (and Leopard, boy that’s confusing.)
There have been conflicting reports about Java on Leopard. Many have complained about a lack of Java 6, some have said that Java 5 is broken too, and others have said Java 5 works just fine. The Spitzer Science Site itself is saying:
Spot and Leopard have not yet been tested under Mac OSX 10.5 (Leopard). We strongly recommend that users not upgrade their OS prior to the Cycle-5 proposal deadline.
That seems like very sound advice.
Update I just tested Spitzer Leopard, seems to work fine in … Leopard. Spot seems to work too, but I did not in anyway test in rigorously. I wouldn’t upgrade before the proposal deadline, just to be safe.
Tags: java, Leopard, spitzer, spot — .
So, you’ve seen the highly annoying Intellitxt ads, possibly on the UK Macworld site or elsewhere. Some sites let you turn them off but there’s no way to turn them off everywhere. I think I figured out how to stop them, at least on a Mac.
You’ll need to edit your /etc/hosts file and add this line:
127.0.0.1 images.intellitxt.com
And then you’ll need to flush the lookupd cache with a
sudo lookupd -flushcache
This prevents the javascript from loading from the intellitxt ads and thus, stops them from happening. Now, I know there are some ethical questions with blocking ads on web sites, since advertising (even on my own site) helps to pay the bills, etc. But, these ads are invasive and highly annoying (which is why I don’t have any here), so I think turning them off is something worth doing.
Update Some other options for blocking these ads can be found here.
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A new SDK for Papers is out that allows developers (or anyone) to write search engine plugins for Papers, the excellent journal paper management program that I have mentioned previously. Alas, I know next to nothing about Mac programming, so try as I might to understand the SDK and how to make a plugin that let us search ADS from within Papers, it looks beyond my abilities.
So, maybe someone out there reading this would like to give it a shot?
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The wonderful High performance computing for Mac site has pre-compiled binaries for Grace and the motif library on which it depends. This is perhaps easier than the compile-fest that is required to get it working via Fink on an Intel-based Mac. Of course, for reasons that remain unclear to me, people appear to prefer IDL, SM, and “something else entirely” to grace.
Tags: fink, grace, plotting, unix — .
So, I admit I only recently installed SM(supermongo), and only have used it slightly. Between IDL, grace(installable via Fink or there are binaries for MacOS X at the HPC site), and Plot, I just don’t see why any Mac user would make plots in SM. It requires gnuplot-esque scripts/programs, and just seems in general a pain and esoteric.
Perhaps it is powerful, perhaps for automated plot creation from certain kinds of data, it’s great, but I don’t understand its popularity. Has anyone used all the above tools and yet prefers SM? If so, please post a comment. I’m curious if I’m missing something.
For casual plotting, say from analysis that I do in IDL, I just do quick plots in IDL itself, and I’ve written a fair number of simple IDL routines that call plot or ploterr or other people’s plotting programs. This works for day to day plotting, and is easy to integrate into my other IDL programs. For almost all plots for publication, I have always used the aforementioned grace, which I installed with Fink.
If if I wasn’t already familiar with grace, I’d probably try this unfortunately under-named program, Plot. It seems pretty good, but since it’s very similar to Grace except with all the options in different places, so I’ve just stayed with the familiar Grace. But, I vastly prefer a graphical interface like this for tweaking than altering parameters via some script. I have also used gnuplot. It was a nightmare. I recreated in grace in one hour what it took days to get gnuplot to do, and do poorly. I abandoned gnuplot as a first year grad student.
Anyway, I know sm must have its fans, so if that’s you, let me know why you like it below. But, please note if you’ve used any other plotting program.
Update I’m baffled by the “something else entirely” winning unless it’s non-astronomers voting for Excel. Whatever you are voting for, could you post a comment and tell me? Also, I recently got a new Macbook, and installing Grace via Fink was a royal pain requiring a selfupdate via rsync and then a very long compile-fest because they don’t have a binary available. It’s hard to recommend with all that pain, but I maintain it’s much better than SM.
Update II Ploticus sounds vaguely familiar (see in the comments), but not so much python/matplotlib. These sound like IDL/SMish sort of plotting though. Personally, I still prefer a GUI – hence my like for xmgr Grace.
Update III I certainly get the desire to have a plot automagically made while one is doing data reduction, analysis, etc. This is one reason I like IDL. However, I prefer to be able to finely tune the appearance in a GUI for a plot designed for publication. I suppose it’s a learning curve thing. Granted, once you write one sm script to plot a spectra … you’re set for all other spectra. However, I’m not convinced for my own work that the time/effort spent learning how to write such a script is worth it, since I’m obviously rather comfortable with Grace. (It’s worth noting for a certain repetitive plots I have used IDL.)
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Updates at the bottom
The somewhat poorly named Papers 1.1 won an Apple Design Award today. The program is designed to help scientists track the bazillion PDFs of various journal articles we download. Unfortunately, it integrates with PubMed (I don’t even know what that is but presumably for medical journals?) but not ADS. However, it has a plugin architecture and an SDK so maybe somehow someone can make a NASA ADS plug in for it. And, the developers are taking suggestions for other databases.
However, in any event, it’s $39. (Try doing a google search for for papers ads plugin and you’ll see what I mean by not being named well … ADS isn’t the best abbrevation either.) Updated – Students can get a 40% discount.
A more generic “iPhoto for PDFs” is the $34 Yep. You can tag, search the content, and organize your PDFs. No attempt at helping you build bibliographies, etc., though. (Papers presumably can export to bibtex, but I don’t know how well that’ll work if it’s not grabbing tags from ADS).
I plat to try out both programs and then write a little more. Yep, for example, will just find all the PDFs in folders you specify. You can include specific folders or exclude them too. Perhaps you don’t want Yep to keep track of figures … or perhaps you can never find where you saved the PDF figure you made and you do want it to track figures.
While I’m mentioning these programs, there’s also the more generic “store anything” program Yojimbo which has a much broader scope but also can store and catalog PDFs, though it doesn’t just track all the PDFs you have wherever they are, the way Yep does.
Update 1 Ok, Papers may actually be pretty good. I imported my dissertation .bib bibtex file and it parsed it without any trouble. Now, it of course didn’t magically know where the local PDF was, but it did have the URL which was in the .bib file. So, it has its own webkit powered web browser and took me to the journal’s page (say, ApJ). At which point if I clicked on the PDF link it automagically downloaded the PDF, stored it locally, and associated it with the proper entry in Papers’ library. Nice. Though, it doesn’t understand the NASA ADS based bibtex abbreviations so things look like \apj and such.
Update 2 Apple doesn’t give their design awards to chumps. The full-screen PDF viewing feature of Papers is nice; the whole program seems quite useful.
Update 3 Ok, it actually doesn’t use the URL in the bibcode entries but uses the DOI, so papers without a DOI (namely, several PASP papers I tried) Papers could not find online. Even though, the bibtex had an adsurl entry that would point it to the ADS abstract. So, that is somewhat disappointing, but presumably it’s something they can fix without much trouble.
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