I finally processed agpy through sphinx and made some nice html documentation. http://agpy.googlecode.com/svn/trunk/doc/html/agpy.html
LaTeX: VIM + Skim
macvim-skim-install.sh is my install script for using MacVim.app with Skim.app. The agpy wiki page has instructions that are probably more clear; I don't really like the colorscheme / layout of this blog. You can use synctex to make an editor and viewer work together, but it is far from easy and far harder than it should be. Forward-search is pretty easy, but the latex-suite \ls only works intermittently and is not easily customizable. I had to do the following: For VIM->Skim.app (Skim.app is necessary for any of this to work), add these commands to .vimrc:
" Activate skimmap ,v :w<CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR><CR>map ,p :w<CR>:silent !pdflatex -synctex=1 --interaction=nonstopmode %:p <CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR><CR>map ,m :w<CR>:silent !make <CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR><CR>" Reactivate VIMmap ,r :w<CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR>:silent !osascript -e "tell application \"MacVim\" to activate" <CR><CR>map ,t :w<CR>:silent !pdflatex -synctex=1 --interaction=nonstopmode %:p <CR>:silent !/Applications/Skim.app/Contents/SharedSupport/displayline -r <C-r>=line('.')<CR> %<.pdf %<CR>:silent !osascript -e "tell application \"MacVim\" to activate" <CR><CR>The ,m command will reload the file and put your cursor where the text is. ,t will return VIM to the front afterwards. Going the other way (reverse-search / inverse-search) was MUCH more challenging. The code that does this is on agpy. Reproduced here for posterity (I hope to update the agpy version to deal with tabs). [A few hours later, I HAVE replaced the code. Below are the old applescript version, then the new, vim-based version #!/bin/bashfile="$1"line="$2"[ "${file:0:1}" == "/" ] || file="${PWD}/$file"# Use Applescript to activate VIM, find file, and load it# the 'delay' command is needed to prevent command/control/shift from sticking when this# is activated (e.g., from Skim, where the command is command-shift-click)## key code 53 is "escape" to escape to command mode in VIMexec osascript \-e "delay 0.2" \-e "tell application \"MacVim\" to activate" \-e "tell application \"System Events\"" \-e " tell process \"MacVim\"" \-e " key code 53 "\-e " keystroke \":set hidden\" & return " \-e " keystroke \":if bufexists(bufname('$file'))\" & return " \-e " keystroke \":exe \\\":buffer \\\" . bufnr(bufname('$file'))\" & return " \-e " keystroke \":else \" & return " \-e " keystroke \":echo \\\"Could not load file\\\" \" & return " \-e " keystroke \":endif\" & return " \-e " keystroke \":$line\" & return " \-e " end tell" \-e "end tell" New code: download link A
#!/bin/bash# Install directions:# Put this file somewhere in your path and make it executable# To set up in Skim, go to Preferences:Sync# Change Preset: to Custom# Change Command: to macvim-load-line# Change Arguments: to "%file" %linefile="$1"line="$2"debug="$3"echo file: $fileecho line: $lineecho debug: $debugfor server in `mvim --serverlist` do foundfile=`mvim --servername $server --remote-expr "WhichTab('$file')"` if [[ $foundfile > 0 ]] then mvim --servername $server --remote-expr "foreground()" if [[ $debug ]] ; then echo mvim --servername $server --remote-send ":exec \"tabnext $foundfile\" "; fi mvim --servername $server --remote-send ":exec \"tabnext $foundfile\" " if [[ $debug ]] ; then echo mvim --servername $server --remote-send ":$line "; fi mvim --servername $server --remote-send ":$line " fidoneSave that as an executable in your default path (e.g., /usr/local/bin/macvim-load-line) and open Skim.app, go to Preferences:Sync and make the command look like this:
You need to have mvim on your path. mvim comes with MacVim.app, but is NOT installed by default. Install it by doing something like: `` cp /Users/adam/Downloads/MacVim-7_3-53/mvim /usr/local/bin/mvim `` You'll also need to install WhichTab.vim in your ~/.vim/plugins/ directory. It's available here (download link B). Here's the source:
function! WhichTab(filename) " Try to determine whether file is open in any tab. " Return number of tab it's open in let buffername = bufname(a:filename) if buffername == "" return 0 endif let buffernumber = bufnr(buffername) " tabdo will loop through pages and leave you on the last one; " this is to make sure we don't leave the current page let currenttab = tabpagenr() let tab_arr = [] tabdo let tab_arr += tabpagebuflist() " return to current page exec "tabnext ".currenttab " Start checking tab numbers for matches let i = 0 for tnum in tab_arr let i += 1 echo "tnum: ".tnum." buff: ".buffernumber." i: ".i if tnum == buffernumber return i endif endforendfunctionfunction! WhichWindow(filename) " Try to determine whether the file is open in any GVIM *window* let serverlist = split(serverlist(),"\n") "let currentserver = ???? for server in serverlist let remotetabnum = remote_expr(server, \"WhichTab('".a:filename."')") if remotetabnum != 0 return server endif endforendfunctionMontage wrapper
(I'm going to try to gradually shift my blogging to this one...) I wrote a bash wrapper for Tom Robitaille's montage wrapper to allow fits wildcards. #!/bin/bashorigdir=`pwd`#echo $# $*if [ $# -gt 0 ]then for ii in $* do if [ ${ii%=*} == 'header' ] then /usr/local/bin/montage/mGetHdr ${ii#*=} mosaic.hdr elif [ ${ii%=*} == 'outfile' ] then outfile=${ii#*=} elif [ `echo $ii | grep =` ] then params="$params,${ii%=*}='${ii#*=}'" elif [ `echo $ii | grep ".fits"` ] then files=( ${files[@]} $ii ) fi donefiecho ${files[@]} ${#files} if [ ${#files} -gt 0 ] then mkdir tmp cp ${files[@]} tmp/ cp mosaic.hdr tmp/ cd tmp/fiif [ -f mosaic.hdr ] then echo "mosaic.hdr exists, continuing" dir=`pwd` echo python -c "import montage; montage.wrappers.mosaic('$dir','$dir/mosaic',header='$dir/mosaic.hdr'$params)" python -c "import montage; montage.wrappers.mosaic('$dir','$dir/mosaic',header='$dir/mosaic.hdr'$params)" cd $origdir if [ -d tmp ] then if [ $outfile ] then mv tmp/mosaic/mosaic.fits $outfile else mv tmp/mosaic mosaic fi rm -r tmp fielse echo "mosaic.hdr does not exist. Quitting." cd $origdirfi
NaN-friendly convolution
NaN-friendly convolution is important for, e.g., masked data sets in which you want to interpolate across the masked region.
Astropy has gained this functionality with pull request 155: https://github.com/astropy/astropy/pull/155 but this is a "direct" convolution parallel to IDL's 'convol' routine.
My FFT-based version now works in N dimensions and is a little cleaner: http://code.google.com/p/agpy/source/browse/trunk/AG_fft_tools/convolve_nd.py
I'm still working on writing unit tests, and I'm really not sure what the "correct" behavior at the edges is for the different cases... right now, it seems counterintuitive to me, but the code is doing what I expect it to.
Also, Boxcar kernels always result in shifts for me... they're never supposed to. This is a bug.
Currently, other links to these codes: http://stackoverflow.com/questions/1100100/fft-based-2d-convolution-and-correlation-in-python/8454010#8454010
pyspeckit: an astronomical spectroscopic toolkit
Jordan and I have been working on our python-based spectroscopic analysis tool for a while now: pyspeckit is a pretty awesome, now functional but incomplete (and incompletely documented) tool.
specanpy
AG There are now 2 clones of PySpecKit: sPecAnPy Spectroscopic Toolkit (Astronomy)
Testing trackbacks?
I just want to see if "trackbacks" work at all. I recently posted about histograms on google spreadsheets. While I'm at it, might as well throw up a link to my google code site.
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