Merge pull request #107 from pcubillos/pnames

Pnames

MCcubed/VERSION.py

@@ -4,4 +4,4 @@
 # MC3 Version:
 MC3_VER =  2  # Major version
 MC3_MIN =  3  # Minor version
-MC3_REV = 23  # Revision
+MC3_REV = 24  # Revision

MCcubed/mc/driver.py

@@ -29,7 +29,7 @@ def mcmc(data=None,     uncert=None,     func=None,      indparams=None,
          fgamma=None,   fepsilon=None,   hsize=None,     kickoff=None,
          plots=None,    ioff=None,       showbp=None,
          savefile=None, savemodel=None,  resume=None,
-         rms=None,      log=None,        pnames=None,    figpnames=None,
+         rms=None,      log=None,        pnames=None,    texnames=None,
          full_output=None, chireturn=None,
          cfile=None,         parname=None):
   """
@@ -147,10 +147,10 @@ def mcmc(data=None,     uncert=None,     func=None,      indparams=None,
      Configuration file name.
   pnames: 1D string ndarray
      List of parameter names (including fixed and shared parameters)
-     to display on output screen and figures.  See also figpnames.
+     to display on output screen and figures.  See also texnames.
      Screen output trims up to the 11th character.
-     If not defined, default to figpnames.
-  figpnames: 1D string iterable
+     If not defined, default to texnames.
+  texnames: 1D string iterable
      Parameter names for figures, which may use latex syntax.
      If not defined, default to pnames.
   parname: 1D string ndarray
@@ -418,9 +418,9 @@ def parse():
   group.add_argument("--pnames",   dest="pnames", action="store",
                      type=mu.parray, default=None,
                      help="List of parameter names for screen output (and "
-                          "figures if figpnames is not defined).  If pnames "
-                          "is not defined, default to figpnames.")
-  group.add_argument("--figpnames",   dest="figpnames", action="store",
+                          "figures if texnames is not defined).  If pnames "
+                          "is not defined, default to texnames.")
+  group.add_argument("--texnames",    dest="texnames", action="store",
                      type=mu.parray, default=None,
                      help="List of parameter names for figures (may use "
                           "latex syntax). [default: None]")

MCcubed/mc/mcmc.py

@@ -38,7 +38,7 @@ def mcmc(data,          uncert=None,    func=None,      indparams=[],
          fgamma=1.0,    fepsilon=0.0,   hsize=1,        kickoff='normal',
          plots=False,   ioff=False,     showbp=True,
          savefile=None, savemodel=None, resume=False,
-         rms=False,     log=None,       pnames=None,    figpnames=None,
+         rms=False,     log=None,       pnames=None,    texnames=None,
          full_output=False, chireturn=False,
          parname=None):
   """
@@ -144,10 +144,10 @@ def mcmc(data,          uncert=None,    func=None,      indparams=[],
      Filename or File object to write log.
   pnames: 1D string iterable
      List of parameter names (including fixed and shared parameters)
-     to display on output screen and figures.  See also figpnames.
+     to display on output screen and figures.  See also texnames.
      Screen output trims up to the 11th character.
-     If not defined, default to figpnames.
-  figpnames: 1D string iterable
+     If not defined, default to texnames.
+  texnames: 1D string iterable
      Parameter names for figures, which may use latex syntax.
      If not defined, default to pnames.
   full_output:  Bool
@@ -261,14 +261,14 @@ def mcmc(data,          uncert=None,    func=None,      indparams=[],
     uncert = np.ones(ndata)
 
   # Setup array of parameter names:
-  if   pnames is None     and figpnames is not None:
-    pnames    = figpnames
-  elif pnames is not None and figpnames is None:
-    figpnames = pnames
-  elif pnames is None     and figpnames is None:
-    pnames = figpnames = mu.default_parnames(nparams)
-  pnames    = np.asarray(pnames)
-  figpnames = np.asarray(figpnames)
+  if   pnames is None     and texnames is not None:
+    pnames    = texnames
+  elif pnames is not None and texnames is None:
+    texnames = pnames
+  elif pnames is None     and texnames is None:
+    pnames = texnames = mu.default_parnames(nparams)
+  pnames   = np.asarray(pnames)
+  texnames = np.asarray(texnames)
 
   # Set uncert as shared-memory object:
   sm_uncert = mpr.Array(ctypes.c_double, uncert)
@@ -706,13 +706,13 @@ def mcmc(data,          uncert=None,    func=None,      indparams=[],
     else:
       bestfreepars = None
     # Trace plot:
-    mp.trace(Z, Zchain=Zchain, burnin=Zburn, pnames=figpnames[ifree],
+    mp.trace(Z, Zchain=Zchain, burnin=Zburn, pnames=texnames[ifree],
         savefile=fname+"_trace.png")
     # Pairwise posteriors:
-    mp.pairwise(posterior,  pnames=figpnames[ifree], bestp=bestfreepars,
+    mp.pairwise(posterior,  pnames=texnames[ifree], bestp=bestfreepars,
         savefile=fname+"_pairwise.png")
     # Histograms:
-    mp.histogram(posterior, pnames=figpnames[ifree], bestp=bestfreepars,
+    mp.histogram(posterior, pnames=texnames[ifree], bestp=bestfreepars,
         savefile=fname+"_posterior.png",
         percentile=0.683, pdf=pdf, xpdf=xpdf)
     # RMS vs bin size:

docs/mctutorial.rst

@@ -281,16 +281,16 @@ The ``pnames`` argument (optional) define the names of the model
 parametes to be shown in the scren output and figure labels.  In
 figures, the names can use LaTeX syntax.  The screen output will
 display up to 11 characters.  Thus, the user can define the
-``figpnames`` argument (optional), display the appropriate syntax for
+``texnames`` argument (optional), display the appropriate syntax for
 screen output and figures, for example:
 
 .. code-block:: python
 
-   pnames    = ["log(alpha)", "beta", "Teff"]
-   figpnames = [r"$\log(\alpha)$", r"$\beta$", r"$T_{\rm eff}$"]
+   pnames   = ["log(alpha)", "beta", "Teff"]
+   texnames = [r"$\log(\alpha)$", r"$\beta$", r"$T_{\rm eff}$"]
 
-If ``figpnames`` is ``None``, it defaults to ``pnames``. If ``pnames``
-is ``None``, it defaults to ``figpnames``.  If both arguments are
+If ``texnames`` is ``None``, it defaults to ``pnames``. If ``pnames``
+is ``None``, it defaults to ``texnames``.  If both arguments are
 ``None``, they default to a generic ``[Param 1, Param 2, ...]`` list.
 
 .. _walk: