Quote of the day: caterpillar blood

Girl I work with says today: "Caterpillars have the weirdest coloured blood of any animal I've squished and looked at."

Lexan: MEC pulls water bottles

I posted about plastic water bottles a little while ago as it seemed like I was running across more and more information indicating that the Bisphenol-A in Lexan plastic (a common hard, clear, and easily coloured plastic) could be leeching into the water. Lately (in Canada at least) there has been a lot of press about this, in particular with respect to the use of this plastic in baby's bottles.

Today I see that Mountain Equipment Co-op has responded to concerns over Lexan by pulling food storage products made with the plastic until the government provides guidance regarding possible health risks.

While I'm glad to see a company that prides itself on social and environmental responsibility taking some action given the uncertainty about this product, I hope this isn't an example of an over-reaction in the absence of proper information.

I love film

L'Amour embrassant l'Amitie, originally uploaded by physics*chick.

I finally got around to getting my film from Europe developed and actually managed to go pick up the prints. These rolls, especially the black and white, have reminded me again why I love film so much. There is grain, but it is unobtrusive. Really, it only shows up in the very bokeh-y backgrounds of the shallow focal depth shots, the sharp detail is never obscured. The balance of light and shadow is so much stronger. I photograph light, really I do. I think this is why I don't care that I don't have a good flash. I'm rarely moved to take a shot unless I have great light. The sculpture gallery of the Louvre has the most fantastic light. I could have stayed for hours just there sitting in the warm sun and watching the shadows dance off the walls and sculptures.

If you're interested, head over to my Flickr photostream, or directly to my Olympus OM-1 set for just the film photos.

why i hate computers...

... because they *should* help you automate things, but it never seems to work out that way.

I've been doing data analysis on large batches of data files (100's, not 10's, not 1000's) lately, and while I've written an IDL program to do the fitting, plotting, and output of parameters I need, there remained a few tasks that I couldn't figure out how to automate:

1. prepare the batch file (unfortunately, the files are not entirely sequential, so it's not that easy to automate... I could pull some trick with getting a file list and going from there... but...)
   
2. convert all of the .eps files that IDL outputs to .pdf so that I can actually use/view/print them
   

I decided not to bother about the batch file, it didn't really take that long, and once made I save it and never touch it again. BUT the only way I seemed to be able to convert the eps to pdf was to open all the eps files in Preview (it converts them on opening) and then save each of them. This is fine for a few eps (or ps) files... but when you have a 136 staring you in the face and know there are more to come... and that each one involves pressing command-w, enter, enter, you want to find a way that avoids causing tendonitis. Seriously.

First I turned to Automator (I'm a Mac user... unfortunately my solutions will be less than helpful for Linux users, and nearly useless for Windows users... sorry!). To be fair, I have actually managed to get Automator to do some useful things recently, but usually my encounters with the cute little robot leave me feeling rather let down. A quick perusal turned up what I thought was true anyhow, that Automator has no built in way to convert eps (or ps) to pdf. I also checked the Apple Automator downloads and Automator World to no avail.

So I thought, hey, I've got unix commands up the wazoo on here, there *must* be one that can convert eps to pdf...

pstopdf

excellent. So I pull up the man page, figure out how to use it, test it on a couple of files, and merrily enter:

pstopdf *.eps

uuh... geeee... that was fast. A quick "ls" showed me why... it only did the first file. Bugger. A bit of frigging around later, it was determined that pstopdf does not take multiple file arguments.

Ok. That stinks, but maybe now Automator can do something for me using the action "Run Shell Script". Yes, that's it, I'll grab the filenames with a "Find Finder Items" input it to "Run Shell Script" to run the pstopdf command, and voila, there will be 136 pdf's waiting for me. Right? Well not so simple, but yes, eventually. The two main quirks I had to overcome were:

• Apparently at some point the file output and file input of "Find Finder Items" and "Run Shell Script" became mismatched. Oddly this can be solved by inserting a "Label Finder Items" between (you can select none, so it appears to do nothing) which mysteriously does indeed change the file listing in the correct manner.
  
• When using the "Run Shell Script" action: do not enter anything into the script box until after you selected how you wish to pass the input from the previous action. That little drop down will insert the necessary script fragments you need to work with, but only if the box is empty. Since I tend to dive in, I of course immediately put my command in before selecting this, and got very frustrated very quickly.
  
• Also, since the pstopdf command only takes one input at a time (and I couldn't get it to work with stdin, though the man page claims it should function) I used the "Pass input: as arguments" option and placed the pstopdf command inside the loop with "$f" as the argument where the input file should go. If you have a command that takes multiple inputs, you *should* be able to use "$@" outside the loop.
  

Long story short, I'll make available to you, the fruits of my frustration, all for the low, low price of *FREE* (err, uhh, and listening to my rant)... better yet, I'll include my other workflows that I've been using:

• Automator workflow to convert eps (or ps) to pdf (can also be saved as a Finder action)
  
• Automator workflow to take all pdf files in a folder and merge them into a single pdf
  
• Automator workflow to take text files, cut out the header and combine them into a single text file (this one will take some tweaking of the inputs the actions have... easy stuff, just change the drop downs and fields you need)
  

Since some people were having trouble downloading the workflows above, I've put the workflow to convert eps to pdf and to combine pdfs into a zip file for download: PDFworkflows.zip

Is that all? Oh no... no, no, my friends. I started many hours ago, this morning, with IDL opening into an xterm completely UNCONFIGURED for my needs. Let's look at my "needs":

1. Something more readable for my not yet caffinated eyes than black on white (I like a nice soothing green on charcoal... reminds me of that old Apple//c we had when I was a kid)
   
2. More pressing: a bigger window (ok, I can drag and resize, but sometimes funky things happen when I do that)
   
3. And pure luxury would be a SCROLLBAR... yes I like to scroll, especially when I'm running batches of 136 files and I'd like to look at some of that output.
   

Is that too much to ask? I have my X11 configured to open an xterm that is more pleasing on the eyes, but since IDL launches it's own xterm from a mini-app, and I couldn't find where it actually did that anywhere I was stuck with what it gave me. Until today people, until today. All one needs to do is create a default xterm style you are happy with and then any program launching it's own xterm will use this default style. The trick is simple: create a .Xdefaults file in your home directory. The bits of code I used were:

XTerm*background:grey15
XTerm*foreground:PaleGreen
XTerm*vt100*geometry:160x48
XTerm*scrollBar:on
XTerm*scrollKey:on
XTerm*jumpScroll:on
XTerm*saveLines:500
XTerm*cursorColorBackground:DimGray
XTerm*cursorColor:DarkSeaGreen3
XTerm*highlight:LemonChiffon
XTerm*borderColor:SlateGrey

I got most of the commands from here and there is an xterm color table here. Now it looks like this:



Now go make a beautiful, scrollable xterm and make me proud... I have to believe I didn't waste my day in vain.

And convert some eps files to pdf while you're at it. Hell, convert a whole bunch of them and put them together into one gigantic pdf!

Because today, I got my computer to do what I wanted it to do... It just took a really long time.

PhD comics at McGill

the puckwhacker 2000(TM), originally uploaded by physics*chick.

So, two weeks ago I got an email from another member of our group who had just realized that the ticket he had for Jorge Cham's "Power of Procrastination" talk was at the same time as he had to teach a lab. Lucky me I got his ticket!

Excited as I was, this was also at a time when I had a ton of work to do (more on that later). I went, but as I sat there I started figetting and thinking about all the things I had to do, Jorge started into his (anti?)-motivational talk. He got some laughs with wikifacts about Mcgill (hockey was in there, as were Rutherford and the illustrious Mr. Shatner) and started talking about graduate student life. He talked about graduate student salaries, the emotional states of graduate students (some really sobering statistics there), and other such issues.

But then he started talking about procrastination, and moreover the GUILT of procrastination. That nagging feeling that gee-whiz, I really should be working, that is oh so hard to escape, because there's always something more to do, to read, to think about. And I sat there laughing half-heartedly, and wondering if it was really a good idea to have taken 2 hours out of the middle of the afternoon to go see a cartoonist talk about procrastination... guilt. Doh. This is why phd comics is so good... it's funny because it's true.

He ended though by talking about "the thesis" and actually getting to that day where you finally get to play through the "doctor" "doctor" jokes, and the reality that most people aren't actually that happy with their PhD theses, and usually "finishing" a PhD has a lot less to do with being done, and a lot more to do with external factors. Having just made the mental transition from being "in the middle" to "finishing", and having undergone somewhat of an existential crisis over what it "means" to get a PhD this was reassuring for me, and probably has helped keep me on the "finishing" track over the last two hellish weeks of post-doc fellowship applications, paper submission, and conference preparation.

So, naturally, after the talk, I had to get something signed. I bought one of the books of course, but I wanted something else, something special. I got back to the lab and took a look around and spied my hockey stick sitting in the corner waiting for our first game that night. Of COURSE! My labmates thought I was a total weirdo, but whatever. I brought my stick over, and not only did he sign, no, he made it funny. My stick shall henceforth be known to all as "the PUCKWHACKER 2000(TM)". Best procrastination ever!

ps- I'd like to say we won our the game that night, and that I scored a zillion goals with the puckwhacker, but sadly, no, we lost. We lose all our games. Never name a team "Absolut Zero" if you are likely to live up to it!

Where did I go?

Eurotrip Summary, originally uploaded by physics*chick.

Litterally? Well here you go, a summary in pictures. Conferences in beach towns are awesome.

Since I've been back I've been recovering from a cold, going to PhD comics guy's talk (more on that later), and trying to complete a lot of big things. Blogging's been kind of low on the prioity list lately.

Oh yeah, and for you knitting readers out there? I'm finally on Ravelry, so if you're there look for "thenerdynitter" (sorry if anyone out there is theknerdyknitter, or thenirdynitter or some such combination of mispelled words, I didn't know how to check if you were already in there!)

where i've been... under a rock

under a rock, originally uploaded by physics*chick.

Lack of intelligble blog posts due to a general lack of intelligibleness. Instead I present you with a photo I took months ago, made new again with dumpr.net's turn-my-photo-old tool. Makes me kinda want a Holga... but then my obsession with cameras is a whole other issue, and we don't need to go there today.

In other news, I'm chipping away at that to do list for August. However, now that things have settled down a bit compared to the rest of the summer, and most of the key items are either done or mostly done, I'm starting to slow down and relax more.

Quotes of the day: life in Montreal

Hammer rats: a breed of rats which are not seen and infest apartment buildings hammering on the walls, floors and ceilings.

***
hubby: "Living in Montreal is like having a roommate you don't like... that follows you everywhere."
***
hubby: "I need to buy a Land Rover, so I can rove the land."

what's it to you?

what's it to you?, originally uploaded by physics*chick.

Yesterday morning, barely awake, I looked out the window and spotted a little furry creature jotting across the balcony ledge. This "little" guy stopped to sniff the trellis of morning glories to determine if there was anything worth eating and then dissappeared down the side of the building.

If I hadn't taken pictures I'm not sure I'd have believed it once awake.

quick motivational progress update

I feel like I'm doing pretty good with my August sidebar to-do list. I've got 6 things knocked off already, and 3 more in process in other people's hands, I just need to hear back. That's over half of my original to-do list, and not everything on there was small.

But why is the list growing faster than I can get stuff scratched off??? boo.