ps2pdf keep resolution, crop to bounding box

ps2pdf -dEPSCrop -dAutoRotatePages=/None -dAutoFilterColorImages=false -dColorImageFilter=/FlateEncode -dUseFlateCompression=true l007_displaycrop.ps
ref: this post

Making a postscript plot of a gigantic fits image


map = readfits('MOSAIC.fits',hdr)

crpix1 = sxpar(hdr,'CRPIX1')
crpix2 = sxpar(hdr,'CRPIX2')
crval1 = sxpar(hdr,'CRVAL1')
crval2 = sxpar(hdr,'CRVAL2')
cd1_1 = sxpar(hdr,'CD1_1')
cd2_2 = sxpar(hdr,'CD2_2')

x = lindgen(n_e(map[*,0]))
y = lindgen(n_e(map[0,*]))
l = (x-crpix1)*cd1_1+crval1-360
b = (y-crpix2)*cd2_2+crval2

imdisp,map,/axis,xrange=[max(l),min(l)],yrange=[min(b),max(b)],range=[-1,8]


This code makes use of imdisp.pro.

MOSAIC data reduction

MOSAIC reduction is very difficult.
http://www.noao.edu/noao/noaodeep/ReductionOpt/frames.html has the official instructions.

Important things:
Have the latest version of MSCRED and MSCDB installed. Both will give cryptic errors or "cannot open file" errors (because the files don't exist) otherwise.



mscred
setinstrument kpno CCDMosaThin1
msccmatch obj09*.fits coords="!mscgetcat $I $C" search=60 rsearch=1 nfit=30 accept=yes interactive=no fit=no


Site visits, comps

Amusing - visits to my site increased steadily leading up to Jan 9, then crashed precipitously.

LaTeX: replace double quotes with tex quotes

People often make the mistake of putting " in place of `` in LaTeX documents. To repair this, the only easy solution is something like:
s/\(\s\)"/\1``/g
in VIM or sed.

I've seen alternate solutions posted but they're all too complicated. One recommendation was to switch to XeTeX, which sounds like overkill, and others all stated that a complicated perl script is required. The latter is technically true, but why isn't such a thing readily available?

Any other ideas?

Skim: a PDF reader that allows annotations

from Sam: http://skim-app.sourceforge.net/

neat

skill set

is it a marketable skill that I can bring down almost any computer system I'm given access to entirely unintentionally?

post rate

my post rate is too low I need to up it so that my front page doesn't show the same posts any more

scary

I think this is my worst nightmare:
http://antwrp.gsfc.nasa.gov/apod/ap081203.html

LA. Not the smiley.

.inputrc

New unix stuff!

This is, again, stuff I'd searched for forever but never found the right collection of terms. This is what bash readline is REALLY all about.

if you make an inputrc file, you can get awesome readline capabilities (similar to ipython). This post at lifehacker showed me how to do it. This site has a more complete description of how to use readline/inputrc.

Even better: VI command line editing .

There's also something called magic space but I don't know what purpose it serves all the time... it will replace 'magic' characters like !* and !& and !! with whatever command they represent if you hit space immediately after typing them (explained better here).

Wow. Awesome.

MOVIES!

Making movies is surprisingly difficult. No matter what language you use, apparently true movie files can only be made by stringing together images, i.e. there is no native movie-producing feature. Gnuplot can do some simple animations but to do anything sophisticated you need to start delving into variables, and for that I switch to a real language.

So, I returned to python. As usual, it took no more than a few hours of coding and learning to come up with something. But it bothers me that it took that long: I still think python is most deficient in its failure to create a default column-text reader like 'readcol' in IDL. I can't complain that much, though: I wrote my own in about 5 minutes.

Anyway, the key is to use the .set_xdata and .set_ydata functions of a plot to update a canvas. I still don't have nearly as high a plotting speed as I'd like, but it works alright if I don't display to screen. Probably a different backend would be more effective but I don't like to mess with backends.

I use savefig(filename,dpi=50) to reduce the image quality so that it's easier for the animator to handle.

ImageMagick's convert can be used to stitch any kind of image into a movie given that you've installed an mpeg2 encoder (fink gave me mpeg2vidcodec ). The command is very simple:

convert -size 300x300 *.png movie.mpg


I had to use a smaller image size because a series of 1000x12kb files somehow chomped ~6-8 GB of RAM and swap space.

Screen cont'd

Guide to screen

Particularly useful features:

Scrollback:

ctrl-a [
[scroll keys]


Switch to a numbered screen (doesn't work for me so far):

ctrl-a [number]


Ultimate today

We went 2-1 in the tournament, losing the final in a windy game on universe point, 15-14. We won the first game 13-5 or 13-6, and the second by a similarly wide margin. I think I scored 15-20 points on the day and threw an additional few. 2-3 drops and 3-4 throwaways to balance that out. Pretty good on the whole for what was probably my last ultimate of the season.

Of course, that made me very exhausted for the review session this evening. Oh well, I think it worked out. I need to remember to come up with (and post!) a clear explanation of why you can use that silly little triangle to come up with the translation between angle on the sky and image size.

BASH discoveries, readline questions

1. shopt -p
Maybe my hostname completion worked and then stopped working because the bash option hostcomplete was not set. Duh! Why? I don't know. Anyway, shopt -s hostcomplete solves the problem.

nocaseglob is also pretty cool (case insensitive tab completion)

2. it's really hard to search for readline stuff on google. Can anyone explain to me how BASH readline works? I would REALLY like to make bash readline work like ipython, in which you can start typing a command and hit the 'up' key to search through the history for anything beginning with the stuff you've typed up to that point. But I can't even find documentation for the ipython readline! Any hints, anyone?

3. my desktop at work blocks ssh connections. I can ssh into some computers and then into it, but not directly into it.

...as usual, I made a list where not-a-list would have sufficed, and I had to add the last thing because a 2-item list is dumb.

Why do astronomers have such a strong presence on the web?

I'm not making this a complete post, just a few examples of blogs and websites I'm aware of. But we do have a strong presence on the web - astronomers have an unusually high google ranking etc. Is it just because 'we' were here first ('we' excludes me, I'm just jumping on the bandwagon and getting a free ride)?

Examples:
Pamela Gay
Dr Lisa

Science writers who write on astronomy:
Dave Mosher

Photo Contest

http://www.nrao.edu/index.php/learn/gallery/imagecontest

Python magic / advanced numpy indexing

Yeah, indexing python arrays should really be easy.

Stefan van der Walt's page


In [85]: bi = (f.bolo_indices[np.newaxis,:] + zeros([7751,1])).astype('int')

In [86]: whc = (whscan[:,np.newaxis] + zeros([1,107])).astype('int')

In [87]: array2d[whc,bi] = temp2d


Python: one-line arrays

Ahhh, refreshing:

whscan = asarray([arange(scanlen)+i for i in scans_info[:,0]]).ravel()


Not like IDL, which takes at least 4 lines b/c of the variable declaration. There's probably a better way to do that too.

Port vs Fink

Port failed to install:

adam-macbook ~$ sudo port install py25-matplotlib
---> Building py25-hashlib with target build
---> Staging py25-hashlib into destroot
---> Installing py25-hashlib 2.5.2_0
---> Activating py25-hashlib 2.5.2_0
---> Cleaning py25-hashlib
---> Fetching py25-zlib
---> Verifying checksum(s) for py25-zlib
---> Extracting py25-zlib
---> Configuring py25-zlib
---> Building py25-zlib with target build
---> Staging py25-zlib into destroot
---> Installing py25-zlib 2.5.2_0
---> Activating py25-zlib 2.5.2_0
---> Cleaning py25-zlib
---> Fetching py25-setuptools
---> Attempting to fetch setuptools-0.6c8.tar.gz from http://cheeseshop.python.org/packages/source/s/setuptools/
---> Verifying checksum(s) for py25-setuptools
---> Extracting py25-setuptools
---> Applying patches to py25-setuptools
---> Configuring py25-setuptools
---> Building py25-setuptools with target build
---> Staging py25-setuptools into destroot
---> Installing py25-setuptools 0.6c8_2
---> Activating py25-setuptools 0.6c8_2
---> Cleaning py25-setuptools
---> Fetching py25-tz
---> Attempting to fetch pytz-2007k.tar.bz2 from http://cheeseshop.python.org/packages/source/p/pytz/
---> Verifying checksum(s) for py25-tz
---> Extracting py25-tz
---> Configuring py25-tz
---> Building py25-tz with target build
---> Staging py25-tz into destroot
---> Installing py25-tz 2007k_0
---> Activating py25-tz 2007k_0
---> Cleaning py25-tz
---> Fetching py25-dateutil
---> Attempting to fetch python-dateutil-1.4.1.tar.gz from http://labix.org/download/python-dateutil
---> Verifying checksum(s) for py25-dateutil
---> Extracting py25-dateutil
---> Configuring py25-dateutil
---> Building py25-dateutil with target build
---> Staging py25-dateutil into destroot
---> Installing py25-dateutil 1.4.1_0
---> Activating py25-dateutil 1.4.1_0
---> Cleaning py25-dateutil
---> Fetching fftw-3
---> Attempting to fetch fftw-3.1.3.tar.gz from http://www.fftw.org/
---> Verifying checksum(s) for fftw-3
---> Extracting fftw-3
---> Configuring fftw-3
---> Building fftw-3 with target all
---> Staging fftw-3 into destroot
---> Installing fftw-3 3.1.3_0
---> Activating fftw-3 3.1.3_0
---> Cleaning fftw-3
---> Fetching py25-nose
---> Attempting to fetch nose-0.10.4.tar.gz from http://somethingaboutorange.com/mrl/projects/nose/
---> Verifying checksum(s) for py25-nose
---> Extracting py25-nose
---> Configuring py25-nose
---> Building py25-nose with target build
---> Staging py25-nose into destroot
---> Installing py25-nose 0.10.4_0
---> Activating py25-nose 0.10.4_0
---> Cleaning py25-nose
---> Fetching py25-numpy
---> Attempting to fetch numpy-1.2.0.tar.gz from http://downloads.sourceforge.net/numpy
---> Verifying checksum(s) for py25-numpy
---> Extracting py25-numpy
---> Applying patches to py25-numpy
---> Configuring py25-numpy
---> Building py25-numpy with target build
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0" && /opt/local/bin/python2.5 setup.py build " returned error 1
Command output: setup_package()
File "setup.py", line 89, in setup_package
configuration=configuration )
File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/core.py", line 184, in setup
return old_setup(**new_attr)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/core.py", line 151, in setup
dist.run_commands()
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/dist.py", line 974, in run_commands
self.run_command(cmd)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build.py", line 37, in run
old_build.run(self)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/command/build.py", line 112, in run
self.run_command(cmd_name)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build_src.py", line 130, in run
self.build_sources()
File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build_src.py", line 147, in build_sources
self.build_extension_sources(ext)
File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build_src.py", line 250, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build_src.py", line 307, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 87, in generate_config_h
raise SystemError,"Failed to test configuration. "\
SystemError: Failed to test configuration. See previous error messages for more information.

Error: The following dependencies failed to build: py25-numpy py25-tkinter tcl tk
Error: Status 1 encountered during processing.


I don't want to deal with it so I'm just using Fink.

Reinstalling a system

Python died tonight when I foolishly tried to update numpy or matplotlib. One was not compatible with the other in upgraded form, and the update for matplotlib wouldn't install because of GTK issues that were totally opaque.

So, I reinstalled EVERYTHING - fink AND macports - from scratch. If I don't get things running by morning I'm going to have to do a restore, which is ugly as death.

Things I need to do post-install:

sudo port install python_select
sudo python_select python25


test ipython
test matplotlib
test numpy