Merge commit 'alioth/yoh/master' into mh/master

* commit 'alioth/yoh/master':
  NF(BF): MVPA_MATPLOTLIB_BACKEND config variable
  RF: addressed recent Michael's change + few PL issues
  RF+NF: HHS+IP -> HHS+09a, added also HHS+09b, references.txt got regenerated
  BF: proper header for bib2rst_ref tool, more information on exception while decoding unicode

Makefile

@@ -242,8 +242,8 @@ unittests: unittest-nonlabile unittest unittest-badexternals \
 
 te-%: build
 	@echo -n "I: Testing example $*: "
-	@MVPA_EXAMPLES_INTERACTIVE=no PYTHONPATH=. python doc/examples/$*.py \
-	 >| temp-$@.log 2>&1 \
+	@MVPA_EXAMPLES_INTERACTIVE=no PYTHONPATH=. MVPA_MATPLOTLIB_BACKEND=agg \
+	 python doc/examples/$*.py >| temp-$@.log 2>&1 \
 	 && echo "passed" || { echo "failed:"; cat temp-$@.log; }
 	@rm -f temp-$@.log
 

doc/examples/pymvpa.cfg

@@ -46,6 +46,10 @@ interactive = yes
 # which SVM implementation to use by default: libsvm or shogun
 backend = libsvm
 
+[matplotlib]
+# override the default matplotlib's backend
+# backend = pdf
+
 [externals]
 # whether to really raise an exception when an externals test fails _and_
 # raising an exception was requested

doc/misc/references.bib

@@ -253,12 +253,28 @@ @Manual{ HHS+latest
 	address = "Available online at http://www.pymvpa.org/PyMVPA-Manual.pdf"
 }
 
-@Article{ HHS+IP,
+@Article{ HHS+09a,
 	title = "PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data",
 	author = "Michael Hanke and Yaroslav O Halchenko and Per B Sederberg and Stephen José Hanson and James V Haxby and Stefan Pollmann",
 	journal = "Neuroinformatics",
-	year = "in press",
-	pymvpa-summary = "Introduction into the analysis of fMRI data using PyMVPA."
+	year = "2009",
+	pymvpa-summary = "Introduction into the analysis of fMRI data using PyMVPA.",
+	volume = "In press",
+	doi = "10.1007/s12021-008-9041-y",
+	url = "http://dx.doi.org/10.1007/s12021-008-9041-y",
+	pymvpa-keywords = "PyMVPA, fMRI"
+}
+
+@Article{ HHS+09b,
+	author = "Michael Hanke and Yaroslav O. Halchenko and Per B. Sederberg and Emanuele Olivetti and Ingo Fründ and Jochem W. Rieger and Christoph S. Herrmann and James V. Haxby and Stephen José Hanson and Stefan Pollmann",
+	title = "{PyMVPA}: A Unifying Approach to the Analysis of Neuroscientific Data",
+	journal = "Frontiers in Neuroinformatics",
+	year = "2009",
+	pymvpa-summary = "Demonstration of PyMVPA capabilities concerning multi-modal or modality-agnostic data analysis.",
+	volume = "In press",
+    doi = "10.3389/neuro.11.003.2009",
+    url = "http://dx.doi.org/10.3389/neuro.11.003.2009",
+	pymvpa-keywords = "PyMVPA, fMRI, EEG, MEG, extracellular recordings"
 }
 
 @Article{ PMB+IP,
@@ -268,4 +284,3 @@ @Article{ PMB+IP
 	year = "in press",
 	doi = "10.1016/j.neuroimage.2008.11.007"
 }
-

doc/references.txt

@@ -62,11 +62,26 @@ experiments.
 
 **Hanke, M., Halchenko, Y. O., Sederberg, P. B. & Hughes, J. M.** The PyMVPA Manual. Available online at http://www.pymvpa.org/PyMVPA-Manual.pdf.
 
-.. _HHS+IP:
+.. _HHS+09a:
 
-**Hanke, M., Halchenko, Y. O., Sederberg, P. B., Hanson, S. J., Haxby, J. V. & Pollmann, S.** (in press). PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data. *Neuroinformatics*.
+**Hanke, M., Halchenko, Y. O., Sederberg, P. B., Hanson, S. J., Haxby, J. V. & Pollmann, S.** (2009). PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data. *Neuroinformatics*, *In press*.
   *Introduction into the analysis of fMRI data using PyMVPA.*
 
+  Keywords: :keyword:`PyMVPA`, :keyword:`fMRI`
+
+  DOI: http://dx.doi.org/10.1007/s12021-008-9041-y
+
+
+.. _HHS+09b:
+
+**Hanke, M., Halchenko, Y. O., Sederberg, P. B., Olivetti, E., Fründ, I., Rieger, J. W., Herrmann, C. S., Haxby, J. V., Hanson, S. J. & Pollmann, S.** (2009). PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data. *Frontiers in Neuroinformatics*, *In press*.
+  *Demonstration of PyMVPA capabilities concerning multi-modal or
+  modality-agnostic data analysis.*
+
+  Keywords: :keyword:`PyMVPA`, :keyword:`fMRI`, :keyword:`EEG`, :keyword:`MEG`, :keyword:`extracellular recordings`
+
+  DOI: http://dx.doi.org/10.3389/neuro.11.003.2009
+
 
 .. _HH08:
 

mvpa/base/externals.py

@@ -191,6 +191,7 @@ def __check_pylab_plottable():
           'pywt wp reconstruct fixed': "__check_pywt(['wp reconstruct fixed'])",
           'rpy': "import rpy as __",
           'lars': "import rpy; rpy.r.library('lars')",
+          'matplotlib': "import matplotlib as __",
           'pylab': "import pylab as __",
           'pylab plottable': "__check_pylab_plottable()",
           'openopt': "import scikits.openopt as __",

mvpa/misc/plot/erp.py

@@ -38,7 +38,7 @@ def _offset(ax, x, y):
     """
     d = dir(mlt)
     if 'offset_copy' in d:
-        # XXX not tested but should work ;-)
+        # ??? not tested but should work ;-)
         return mlt.offset_copy(ax.transData, x=x, y=y, units='dots')
     elif 'BlendedAffine2D' in d:
         # some newer versions of matplotlib
@@ -214,7 +214,6 @@ def plotERP(data, SR=500, onsets=None,
         pre_mean = pre
 
     # set default
-    # XXX should this be exposed?
     pre_discard = 0
 
     if onsets is not None: # if we need to extract ERPs
@@ -231,7 +230,6 @@ def plotERP(data, SR=500, onsets=None,
         erp_data = bcm(data)
 
         # override values since we are using Boxcar
-        pre_discard = 0
         pre_onset = pre
     else:
         if pre_onset is None:
@@ -448,6 +446,7 @@ def plotERPs(erps, data=None, ax=None, pre=0.2, post=None,
                  zorder=1, offset=loffset)
 
     def set_limits():
+        """Helper to set x and y limits"""
         ax.set_xlim( (-pre, post) )
         if ylim != None:
             ax.set_ylim(*ylim)

mvpa/suite.py

@@ -23,8 +23,17 @@
 
 
 from mvpa import *
-from mvpa.algorithms.cvtranserror import *
 from mvpa.base import *
+
+# Assure that we are setting up matplotlib's frontend prior to the
+# first import of pylab.
+if externals.exists("matplotlib"):
+    __backend = cfg.get('matplotlib', 'backend')
+    if __backend:
+        import matplotlib
+        matplotlib.use(__backend)
+
+from mvpa.algorithms.cvtranserror import *
 from mvpa.base.config import *
 from mvpa.base.verbosity import *
 

tools/bib2rst_ref.py

@@ -1,5 +1,12 @@
 #!/usr/bin/env python
-
+#emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+#ex: set sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the PyMVPA package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 import _bibtex
 import re
 
@@ -228,8 +235,11 @@ def open(self, filename):
                 # figure out what the last argument really does
                 # leaving in -1 seems to be save
                 value = _bibtex.expand(file, v,  0)[2]
-                value = unicode(value, 'utf-8')
-
+                try:
+                    value = unicode(value, 'utf-8')
+                except UnicodeDecodeError, e:
+                    print "ERROR: Failed to decode string '%s'" % value
+                    raise
                 if k.lower() == 'author':
                     value = value.split(' and ')