W. Trevor King [Sun, 24 Jun 2012 06:51:45 +0000 (02:51 -0400)]
Add labeit95 and sandal09 to root.bib.
W. Trevor King [Sun, 24 Jun 2012 06:49:58 +0000 (02:49 -0400)]
Add apparatus/main.bib with vendor references.
W. Trevor King [Sun, 24 Jun 2012 06:49:07 +0000 (02:49 -0400)]
Add piezo.asy for explaining how a tubular piezo works.
W. Trevor King [Fri, 22 Jun 2012 12:04:22 +0000 (08:04 -0400)]
Add skeletal_muscle.jpg (modified from Wikipedia).
W. Trevor King [Sun, 17 Jun 2012 20:24:06 +0000 (16:24 -0400)]
Whitespace cleanups in the rest of the figures/*/*.asy files.
Used sed to replace tabs with spaces and strip trailing spaces.
W. Trevor King [Sun, 17 Jun 2012 20:21:24 +0000 (16:21 -0400)]
Whitespace cleanups in base_afm.asy and monte-carlo.asy.
W. Trevor King [Sun, 17 Jun 2012 20:18:03 +0000 (16:18 -0400)]
Convert tabs to spaces in expt-sawtooth.asy.
W. Trevor King [Sun, 17 Jun 2012 20:12:12 +0000 (16:12 -0400)]
Relabel unfolding/rate.tex to sec:rate.
This fixes a label-collision with unfolding/distributions.tex on
sec:unfolding-distributions.
W. Trevor King [Sun, 17 Jun 2012 20:07:10 +0000 (16:07 -0400)]
Remove asyprocess references from SConscript files.
W. Trevor King [Sun, 17 Jun 2012 18:23:33 +0000 (14:23 -0400)]
Whitespace cleanups in schematic/unfolding.asy.
W. Trevor King [Sun, 17 Jun 2012 17:54:23 +0000 (13:54 -0400)]
Fix sec:cantilever-calib-intro -> sec:cantilever-calib:intro reference.
W. Trevor King [Sun, 17 Jun 2012 17:54:15 +0000 (13:54 -0400)]
Remove unused asyprocess script (leftover from asyfig framework).
W. Trevor King [Sat, 16 Jun 2012 18:52:46 +0000 (14:52 -0400)]
Create figures/scratch immediately, so it's there by the time we run LaTeX.
W. Trevor King [Sat, 16 Jun 2012 18:51:57 +0000 (14:51 -0400)]
Remove unused asyfig packages.
W. Trevor King [Sat, 16 Jun 2012 16:23:05 +0000 (12:23 -0400)]
Add hong10, zhao10, liu10, measey09, shan09, yuan08, liu08, ... to root.bib.
Papers by Prof. Yang.
W. Trevor King [Wed, 18 Apr 2012 17:24:26 +0000 (13:24 -0400)]
Change my email address from drexel.edu to tremily.us.
W. Trevor King [Thu, 2 Feb 2012 16:46:06 +0000 (11:46 -0500)]
Add new citation ng07b and change ng07 to ng07a.
W. Trevor King [Thu, 2 Feb 2012 15:27:35 +0000 (10:27 -0500)]
Add comments referenceing Brockwell's 2002 paper with respect to Gumbel dist.
W. Trevor King [Sat, 14 May 2011 19:02:07 +0000 (15:02 -0400)]
Remove src/unfolding-distributions/* which were moved to src/unfolding/distributions-*.
W. Trevor King [Sat, 14 May 2011 18:57:59 +0000 (14:57 -0400)]
Update to \DUTmonth and \DUTyear to work with >=drexel-thesis-0.10.
W. Trevor King [Sat, 14 May 2011 18:44:44 +0000 (14:44 -0400)]
Remove silly tex/ directory.
W. Trevor King [Sat, 14 May 2011 18:42:12 +0000 (14:42 -0400)]
Add a PyMOL builder to SCons and generalize PYMOL_PATH setup.
W. Trevor King [Sat, 14 May 2011 18:11:50 +0000 (14:11 -0400)]
Adjust asymptote and gnuplot doctests to be directory independent.
Now you can run the doctests from any directory and they will still
find the files they are scanning to test. Note that SCons may not be
installed in your PYTHONPATH by default:
> From: Steven Knight
> Date: May 28, 2008; 10:01am
> Subject: Re: easy_installed scons not working
>
> ...
>
> In essence, we've tried to make SCons more like a standalone
> application that happens to use Python, instead of a Python
> application that only exists "within" the Python installation itself.
> This separation also allows you, for example, to experiment with
> upgrading your Python version without having to re-install SCons.
>
> ...
>
> Note that the hacking we've done on our setup.py does allow you to
> install into the site-package/ subdirectory if you wish, using an
> extended --standard-lib option.
>
> ...
So you may need to try something like:
PYTHONPATH=/usr/lib/scons-2.0.1/ python site_cons/site_tools/asymptote.py
to run the tests.
W. Trevor King [Sat, 14 May 2011 18:02:01 +0000 (14:02 -0400)]
Correct GNUPLOTLAGS -> GNUPLOTFLAGS typo in site_cons/site_tools/gnuplot.py.
W. Trevor King [Sat, 14 May 2011 17:41:27 +0000 (13:41 -0400)]
Transition from \asyfig to the stock \asyinclude.
W. Trevor King [Sat, 23 Apr 2011 15:12:03 +0000 (11:12 -0400)]
Work around null-dereference bug in some versions of asymptote.
See
http://sourceforge.net/tracker/?func=detail&aid=
3292023&group_id=120000&atid=685683
for details on the bug.
W. Trevor King [Tue, 29 Mar 2011 20:51:37 +0000 (16:51 -0400)]
Fix (a^2-z^2)^2 typo in integrals.tex.
W. Trevor King [Wed, 23 Feb 2011 17:55:12 +0000 (12:55 -0500)]
Begin rearranging chapters and sections following Prof. Yang's suggestions.
W. Trevor King [Sat, 23 Oct 2010 17:27:46 +0000 (13:27 -0400)]
Convert author macro JFernandez -> JMFernandez.
W. Trevor King [Sat, 23 Oct 2010 17:21:59 +0000 (13:21 -0400)]
Condense author aliases for MSZKellermayer and SBSmith.
W. Trevor King [Sat, 23 Oct 2010 16:49:18 +0000 (12:49 -0400)]
Added dates to rief97* which swapped a <-> b.
W. Trevor King [Sat, 23 Oct 2010 16:39:32 +0000 (12:39 -0400)]
Added dates to carrion-vazques99* which swapped a <-> b.
W. Trevor King [Sat, 23 Oct 2010 15:37:55 +0000 (11:37 -0400)]
Fix some long URLs that had been wrapped by pybtex.
W. Trevor King [Sun, 17 Oct 2010 20:58:37 +0000 (16:58 -0400)]
Merge branch 'master' of ssh://einstein/~/public_html/code/git/thesis
W. Trevor King [Sun, 17 Oct 2010 20:54:18 +0000 (16:54 -0400)]
Move src/packages/ to src/package/.
This avoids errors like
TypeError: Tried to lookup Dir 'build/packages' as a File.
when building with older SCons versions.
W. Trevor King [Sun, 17 Oct 2010 20:53:30 +0000 (16:53 -0400)]
Standardize figure size (15cmx10cm) for fit-space/means.gp.
W. Trevor King [Sat, 16 Oct 2010 19:49:46 +0000 (15:49 -0400)]
Give root.bib a final run through pybtex.
This just re-wrapped some author lines and swapped dietz06{a,b} (now
with months and dates to stabilize future sorts).
root.bib is now stable against future pybtex passes.
W. Trevor King [Sat, 16 Oct 2010 19:18:31 +0000 (15:18 -0400)]
Consolidate macros in root.bib.
W. Trevor King [Sat, 16 Oct 2010 17:50:35 +0000 (13:50 -0400)]
Reformatted root.bib with pybtex and rekeyed LaTeX source appropriately.
W. Trevor King [Sat, 16 Oct 2010 17:45:08 +0000 (13:45 -0400)]
More key/name tuning in root.bib.
W. Trevor King [Sat, 16 Oct 2010 17:39:14 +0000 (13:39 -0400)]
Set custom key for NIST:gumbel entry.
W. Trevor King [Sat, 16 Oct 2010 17:31:48 +0000 (13:31 -0400)]
Additional field name cleanups in root.bib.
W. Trevor King [Sat, 16 Oct 2010 17:25:46 +0000 (13:25 -0400)]
Set custom keys for codata entries.
W. Trevor King [Sat, 16 Oct 2010 17:24:32 +0000 (13:24 -0400)]
Set custom keys for uniprot entries.
W. Trevor King [Sat, 16 Oct 2010 17:16:32 +0000 (13:16 -0400)]
Differentiate Best2008 bibtex entries.
W. Trevor King [Sat, 16 Oct 2010 17:13:59 +0000 (13:13 -0400)]
Removed duplicate keywords fields from staple08.
W. Trevor King [Sat, 16 Oct 2010 17:10:52 +0000 (13:10 -0400)]
Remove duplicate note field from ciccotti86.
W. Trevor King [Sat, 16 Oct 2010 17:09:25 +0000 (13:09 -0400)]
Remove duplicate note field from ryckaert77.
W. Trevor King [Sat, 16 Oct 2010 17:07:57 +0000 (13:07 -0400)]
Consolitate duplicate schlierf04 entries.
W. Trevor King [Sat, 16 Oct 2010 17:05:10 +0000 (13:05 -0400)]
Correct DeGrado -> WDeGrado typo.
W. Trevor King [Sat, 16 Oct 2010 17:04:04 +0000 (13:04 -0400)]
Correct <X>BrowerToland -> BDBrowerToland typos.
W. Trevor King [Sat, 16 Oct 2010 17:01:46 +0000 (13:01 -0400)]
Correct VMontant -> VMontana typo.
W. Trevor King [Sat, 16 Oct 2010 17:00:13 +0000 (13:00 -0400)]
Correct MGau -> MGao typo.
W. Trevor King [Sat, 16 Oct 2010 16:58:22 +0000 (12:58 -0400)]
Corrections to root.bib before reformating with pybtex.
W. Trevor King [Sun, 13 Jun 2010 14:20:45 +0000 (10:20 -0400)]
unfolding.asy also needs base_afm.asy.
W. Trevor King [Sun, 13 Jun 2010 14:19:22 +0000 (10:19 -0400)]
Use \text intead of \mathrm in \supScript.
This avoids setting the font explicitly, which allows the superscript
font to match the standard text font.
W. Trevor King [Sun, 13 Jun 2010 14:17:47 +0000 (10:17 -0400)]
Dedicate to Heaven.
W. Trevor King [Sun, 2 May 2010 04:58:48 +0000 (00:58 -0400)]
Added open source highlights to acknowledgments
W. Trevor King [Sun, 2 May 2010 04:30:27 +0000 (00:30 -0400)]
Moved remaining text portions of root.tex into src/blurb/
Main benefits:
* Alias('latex-base') (used by asyprocess) won't change when you edit
the blurbs. Previously, that triggered a recompile of all the
Asymptote graphics (slow).
* root.tex stays nice and clean, and it's easy to find and edit the
blurb you want.
W. Trevor King [Sun, 2 May 2010 03:59:04 +0000 (23:59 -0400)]
Only define \U{} and \E{} workarounds in wtk_graph.asy.
We need redefinitions beacause asymptote missaligns labels if we use
\U{} and \E{} directly. However, lots of \mbox{} and \cdot10^{} cruft
is both ugly and brittle. The reworked units() and new Exp() should
be used instead.
math(string) is a simple replacement for "$"+string+"$" which looks
clearer to me in most cases, so I've added that too.
W. Trevor King [Sun, 2 May 2010 03:22:23 +0000 (23:22 -0400)]
Add fit lines to cantilever-sim/v-dep
Also tab-separate (vs space separate) cantilever-sim/v-dep.d/*
with:
for f in v_dep_*; do
awk 'BEGIN{OFS="\t"}{print $1, $2}' "$f" > tmp && mv -f tmp "$f";
done
W. Trevor King [Sun, 2 May 2010 02:26:26 +0000 (22:26 -0400)]
Converted sim-hist from Gnuplot to Asymptote.
W. Trevor King [Sun, 2 May 2010 02:06:21 +0000 (22:06 -0400)]
Convert kappa-sawteeth from Gnuplot to Asymptote.
Also:
* Cleanup Asymptote scanner rules and add descriptive comments.
* Asymptote scanner rules no longer match directories (e.g. ".").
W. Trevor King [Sun, 2 May 2010 00:06:05 +0000 (20:06 -0400)]
Convert expt-sawtooth from Gnuplot to Asymptote.
Also:
* Stripped old comments from sim-sawtooth.asy
* Added title to sim-sawtooth
W. Trevor King [Sat, 1 May 2010 20:29:06 +0000 (16:29 -0400)]
With the newer x/y column flexibility, remove fig3a-kx.data from king_vs_best
Also:
* added fitlines to that figure
* removed some old cruft that should never have been versioned in
the first place.
W. Trevor King [Sat, 1 May 2010 19:42:08 +0000 (15:42 -0400)]
Converted order-dep from Gnuplot to Asymptote.
This lead to some changes in the Asymptote build system:
* New pyfit approach: site_init.link_pyfit() over old Alias('pyfit').
The Alias approach made path extraction ugly and brittle.
The new approach mirrors link_wtk_graph().
* Adjust graphFile() and pyfit to allow single column (i.e. implicit
x, explicit y) datafiles.
* Adjust pyfit to handle single-parameter fitting.
I also increased the horizontal spacing between the v-dep-sd histogram
insets.
W. Trevor King [Sat, 1 May 2010 02:36:20 +0000 (22:36 -0400)]
Converted sim-sawtooth from Gnuplot to Asymptote.
W. Trevor King [Sat, 1 May 2010 01:45:19 +0000 (21:45 -0400)]
Make v-dep shorter (the caption used to overflow the page)
W. Trevor King [Sat, 1 May 2010 01:17:05 +0000 (21:17 -0400)]
Avoid non-standard macros (they seem to break Asymptote's label alignment)
W. Trevor King [Sat, 1 May 2010 01:03:37 +0000 (21:03 -0400)]
Added histrograms to v-dep-sd, and legends to both v-dep* graphs.
They also get a nice dashed line highlighting the histogram source data.
W. Trevor King [Fri, 30 Apr 2010 13:51:22 +0000 (09:51 -0400)]
Converted figures/v-dep from Gnuplot to Asympote (except for embedded histograms)
W. Trevor King [Fri, 30 Apr 2010 13:39:38 +0000 (09:39 -0400)]
Ensure the 'asytools' and 'pyfit' aliases are defined before working on figures
W. Trevor King [Fri, 30 Apr 2010 13:37:54 +0000 (09:37 -0400)]
Remove figure/scripts duplicate of figure/script (added in
fe7fe60ef30da6cd919ce183b47668552fb10583)
W. Trevor King [Fri, 30 Apr 2010 12:24:41 +0000 (08:24 -0400)]
Fixed tuple-concat error in site_init._recursive_glob_dir
Also:
* Added first option to site_init.include_child_SConscripts()
W. Trevor King [Fri, 30 Apr 2010 12:10:47 +0000 (08:10 -0400)]
Added pyfit script using Python's SciPy module for least-squares fitting
W. Trevor King [Fri, 30 Apr 2010 10:21:32 +0000 (06:21 -0400)]
Pulled subdirs() functionality into it's own fn in site_init.py.
W. Trevor King [Thu, 29 Apr 2010 21:59:57 +0000 (17:59 -0400)]
Generalized wtk_graph functions to allow user-controlled x/y/z columns
W. Trevor King [Thu, 29 Apr 2010 06:33:13 +0000 (02:33 -0400)]
Add Alias('bibtex-files') dependency as SCons' LaTeX scanner doesn't seem to.
W. Trevor King [Thu, 29 Apr 2010 05:59:00 +0000 (01:59 -0400)]
Add king_vs_best dependency rules to SCons build tree
W. Trevor King [Thu, 29 Apr 2010 05:21:10 +0000 (01:21 -0400)]
Rework Alias('asymptote-figures'). Previous implementation didn't build the asyfig targets.
W. Trevor King [Thu, 29 Apr 2010 04:22:09 +0000 (00:22 -0400)]
Adjustments to graphMatrixFile for much smaller output.
New implementation converts input x/y/z arrays to x and y sets
specifying coordinates for a z matrix, which asymptote handles more
cleanly than nominally non-gridded data.
Also fixed palette positioning, which was broken in the previous
implementation.
W. Trevor King [Wed, 28 Apr 2010 22:51:24 +0000 (18:51 -0400)]
Fix exponent "^-1" -> "^{-1}" in fit-valley.asy
W. Trevor King [Wed, 28 Apr 2010 22:44:26 +0000 (18:44 -0400)]
Removed wtk_graph.asy symlink from fit-space
Local wtk_graph creation is handled by link_wtk_graph() in the
SConscript file.
W. Trevor King [Wed, 28 Apr 2010 22:24:18 +0000 (18:24 -0400)]
Converted figures/fit-space/fig.gp to fit-valley.asy.
But the current output PDF is big and slow :(.
W. Trevor King [Wed, 28 Apr 2010 21:56:01 +0000 (17:56 -0400)]
Add Alias('asymptote-figures') for explicit \asyfig dependencies.
Also:
* Use env.Alias and env.Depends vs. the bare SCons.Script forms.
* Add figures/cantilever-sim/loading-rate.asy back to build tree.
W. Trevor King [Wed, 28 Apr 2010 21:22:27 +0000 (17:22 -0400)]
Add dsfont files to src/packages/
W. Trevor King [Wed, 28 Apr 2010 21:18:24 +0000 (17:18 -0400)]
Add explicit dependency thesis -> Alias('extra-packages').
SCons' LaTeX scanner doesn't pick them up automatically as of SCons
v1.3.
W. Trevor King [Wed, 28 Apr 2010 21:13:28 +0000 (17:13 -0400)]
Really build thesis.pdf vs. old dummy Touch command.
W. Trevor King [Wed, 28 Apr 2010 21:11:57 +0000 (17:11 -0400)]
Only add DISPLAY to the SCons build environment if the user has set it
W. Trevor King [Wed, 28 Apr 2010 12:14:53 +0000 (08:14 -0400)]
Merge SCons transition with some Gnuplot->Asymptote work.
Conflicts:
tex/src/figures/cantilever-data/Makefile
tex/src/figures/fit-space/Makefile
tex/src/figures/fit-space/king_vs_best.gp
W. Trevor King [Wed, 28 Apr 2010 12:03:40 +0000 (08:03 -0400)]
Removed Gnuplot portions of cantilever-data/v-dep
W. Trevor King [Wed, 28 Apr 2010 12:02:18 +0000 (08:02 -0400)]
Added untested graphMatrixFile to wtk_graph.asy
W. Trevor King [Wed, 28 Apr 2010 12:01:11 +0000 (08:01 -0400)]
Tranitioned king_vs_best from Gnuplot to Asymptote
W. Trevor King [Wed, 28 Apr 2010 11:58:17 +0000 (07:58 -0400)]
sdfont -> dsfont typo correction
W. Trevor King [Fri, 16 Apr 2010 05:13:21 +0000 (01:13 -0400)]
Transitioned build system from Make to SCons
W. Trevor King [Thu, 8 Apr 2010 18:01:26 +0000 (14:01 -0400)]
Removed fit-space/fit.log
I don't know where it came from, but it's a Gnuplot-generated fit log
from something, so it shouldn't get versioned.
W. Trevor King [Thu, 8 Apr 2010 17:56:36 +0000 (13:56 -0400)]
Add improved extract_fit_valley.py to fit-space Makefile flow
W. Trevor King [Tue, 6 Apr 2010 14:53:41 +0000 (10:53 -0400)]
Use mathds over mathbb for double struck fonts
W. Trevor King [Sun, 4 Apr 2010 22:13:47 +0000 (18:13 -0400)]
Fix DOI for wking10 in root.bib
W. Trevor King [Thu, 1 Apr 2010 02:34:28 +0000 (22:34 -0400)]
Need to run latex between bibtex runs to resolve citation note references