I found that setting
mathtext.fontset : stix
fixed the problem.
Here is the debug-annoying output when mathtext.fontset is not set:
./plotlut2.py lut2.txt "figure 1a"
matplotlib data path /usr/lib64/python2.6/site-packages/matplotlib/mpl-data
loaded rc file /home/jsp/.matplotlib/matplotlibrc
matplotlib version 0.99.1.1
verbose.level debug-annoying
interactive is False
units is False
platform is linux2
loaded modules: ['numpy.lib._iotools', 'xml.sax.handler',
'numpy.core.info', 'distutils', 'matplotlib.errno', 'random',
'subprocess', 'gc', 'matplotlib.tempfile', 'numpy.lib.getlimits',
'ctypes._endian', 'encodings.encodings', 'matplotlib.colors',
'numpy.core.numerictypes', 'numpy.testing.sys',
'numpy.lib.__future__', 'xml', 'fnmatch', 'numpy.ma.operator',
'numpy.ma.cPickle', 'struct', 'numpy.random.info', 'tempfile',
'encodings.codecs', 'base64', 'numpy.linalg', 'matplotlib.threading',
'numpy.testing.operator', 'imp', 'numpy.testing', 'collections',
'numpy.core.umath', 'distutils.types', 'numpy.core.scalarmath',
'functools', 'zipimport', 'string', 'matplotlib.subprocess',
'numpy.testing.os', 'matplotlib.locale', 'numpy.lib.arraysetops',
'numpy.testing.unittest', 'numpy.lib.math', 'encodings.utf_8',
'matplotlib.__future__', 'ssl', 'numpy.testing.re', 'itertools',
'numpy.version', 'numpy.lib.re', 'distutils.re', 'ctypes.os',
'numpy.core.os', 'numpy.lib.type_check', 'matplotlib.os',
'numpy.lib.__builtin__', 'signal', 'numpy.lib.types',
'numpy.lib._datasource', 'numpy.lib.io', 'numpy.ma.extras', 'token',
'numpy.fft.fftpack_lite', 'matplotlib.cbook', 'numpy.core.multiarray',
'numpy.__builtin__', 'dis', 'numpy.lib.itertools', 'cStringIO',
'numpy.ma.core', 'numpy.numpy', 'matplotlib.StringIO', 'locale',
'numpy.add_newdocs', 'distutils.sysconfig', 'xml.sax.urlparse',
'syslog', 'xml.sax.saxutils', 'matplotlib.numpy', 'numpy.lib.sys',
'encodings', 'numpy.ma.itertools', 'abc', 'numpy.ctypes',
'numpy.testing.decorators', 'matplotlib.warnings',
'matplotlib.string', 'numpy.lib.numpy', 'matplotlib.sys', 're',
'numpy.lib._compiled_base', 'threading', 'new', 'numpy.random.mtrand',
'math', 'numpy.fft.helper', 'fcntl', 'numpy.ma.warnings',
'matplotlib.fontconfig_pattern', 'numpy.fft.types', 'UserDict',
'inspect', 'distutils.os', '_ctypes', 'numpy.fft.numpy',
'xml.sax.codecs', 'numpy.lib.ufunclike', 'numpy.lib.info', 'ctypes',
'numpy.lib.warnings', 'ctypes.struct', 'numpy.core.sys',
'numpy.core._sort', 'numpy.os', 'paste', '_functools', '_locale',
'matplotlib.sre_constants', 'numpy.lib.shutil', 'thread', 'StringIO',
'numpy.core.memmap', 'traceback', 'weakref', 'numpy.core._internal',
'numpy.fft.fftpack', 'opcode', 'numpy.linalg.lapack_lite',
'distutils.sys', 'os', 'marshal', 'distutils.version', '__future__',
'_collections', 'xml.sax.types', 'matplotlib.traceback', '_sre',
'unittest', 'codecs', 'numpy.random', 'numpy.linalg.numpy',
'__builtin__', 'numpy.lib.twodim_base', 'matplotlib.copy',
'matplotlib.re', 'numpy.core.cPickle', 'operator', 'sre_constants',
'distutils.string', 'numpy.lib.arrayterator', 'select',
'ctypes._ctypes', 'ctypes.sys', 'matplotlib.datetime', 'posixpath',
'numpy.lib.financial', 'errno', '_socket', 'binascii',
'numpy.core.arrayprint', 'datetime', 'numpy.ma',
'matplotlib.matplotlib', 'os.path', 'tokenize',
'numpy.lib.stride_tricks', 'numpy.core.numpy', 'numpy', '_warnings',
'matplotlib.types', 'numpy.core.defmatrix', 'xml.sax.os', 'cPickle',
'encodings.__builtin__', 'matplotlib.xml', '_codecs',
'numpy.lib.operator', 'numpy.__config__', 'numpy.testing.utils',
'xml.sax.xmlreader', 'numpy.ma.numpy', 'copy', 'numpy.core.re',
'_struct', 'numpy.core.fromnumeric', 'numpy.ctypeslib', 'keyword',
'numpy.lib.scimath', 'numpy.fft', 'numpy.lib', 'numpy.random.numpy',
'posix', 'encodings.aliases', 'numpy.lib.function_base', 'exceptions',
'sre_parse', 'abrt_exception_handler', 'pickle', 'numpy.core.ctypes',
'distutils.distutils', 'copy_reg', 'sre_compile', 'xml.sax',
'_random', 'site', 'numpy.lib.polynomial', 'urllib',
'numpy._import_tools', '__main__', 'numpy.fft.info',
'numpy.core.records', 'numpy.core._dotblas', 'numpy.lib.cPickle',
'numpy.sys', 'matplotlib.weakref', 'urlparse', 'xml.sax.urllib',
'shutil', 'numpy.testing.traceback', 'strop',
'numpy.testing.numpytest', 'numpy.core.numeric', 'numpy.linalg.info',
'numpy.core.defchararray', '_abcoll', 'numpy.core',
'matplotlib.rcsetup', 'matplotlib.time', 'xml.sax._exceptions',
'genericpath', 'stat', '_ssl', 'numpy.lib.index_tricks', 'warnings',
'numpy.lib.utils', 'numpy.lib.shape_base', 'numpy.core.types',
'textwrap', 'sys', 'numpy.core.warnings', 'socket',
'numpy.core.__builtin__', 'ctypes.ctypes', 'numpy.lib.format',
'numpy.lib.os', 'numpy.testing.nosetester', 'types', 'xml.sax.sys',
'matplotlib.distutils', '_weakref', 'numpy.ma.inspect',
'distutils.errors', 'matplotlib', 'linecache', 'matplotlib.shutil',
'numpy.lib.cStringIO', 'time', 'numpy.lib.machar',
'numpy.linalg.linalg', 'matplotlib.pyparsing']
$HOME=/home/jsp
CONFIGDIR=/home/jsp/.matplotlib
Using fontManager instance from /home/jsp/.matplotlib/fontList.cache
backend GTKAgg version 2.16.0
FigureCanvasAgg.draw
RendererAgg.__init__
RendererAgg.__init__ width=640.0, height=480.0
RendererAgg.__init__ _RendererAgg done
RendererAgg.__init__ done
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
findfont: Matching
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
to DejaVu Sans (/usr/share/fonts/dejavu/DejaVuSans.ttf) with score of
0.100000
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg._get_agg_font
RendererAgg._get_agg_font
findfont: Matching
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=16.0
to DejaVu Sans (/usr/share/fonts/dejavu/DejaVuSans.ttf) with score of
0.100000
findfont: Matching
:family=STIXGeneral:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXGeneral (/usr/share/fonts/stix/STIXGeneral.otf) with score of
0.000000
findfont: Could not match
:family=STIXSize1:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Matching
:family=STIXGeneral:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0
to STIXGeneral (/usr/share/fonts/stix/STIXGeneralBol.otf) with score
of 0.000000
findfont: Could not match
:family=STIXSize3:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=STIXSize4:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=STIXSize5:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=STIXSize2:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Matching
:family=STIXGeneral:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0
to STIXGeneral (/usr/share/fonts/stix/STIXGeneralItalic.otf) with
score of 0.000000
findfont: Could not match
:family=STIXNonUnicode:style=italic:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=STIXNonUnicode:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=STIXNonUnicode:style=normal:variant=normal:weight=bold:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=cmb10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=cmtt10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=cmmi10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=cmex10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=cmsy10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=cmr10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
findfont: Could not match
:family=cmss10:style=normal:variant=normal:weight=normal:stretch=normal:size=12.0.
Returning /usr/share/fonts/thai-scalable/Waree-Oblique.ttf
RendererAgg.draw_text
RendererAgg.draw_mathtext
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg.draw_mathtext
RendererAgg._get_agg_font
findfont: Matching
:family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=large
to DejaVu Sans (/usr/share/fonts/dejavu/DejaVuSans.ttf) with score of
0.100000
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg._get_agg_font
RendererAgg.points_to_pixels
RendererAgg.points_to_pixels
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg._get_agg_font
RendererAgg._get_agg_font
RendererAgg.draw_text
RendererAgg.draw_mathtext
FigureCanvasAgg.buffer_rgba
RendererAgg.buffer_rgba