Update kdeplot

doc/auxiliary-tools.rst

@@ -230,8 +230,8 @@ After finishing the calculation, the plot is saved in
 ``lifetime.png``. The black dots show original data points. The
 drawing area is automatically set to make the look good, where its
 higher lifetime side is not drawn if all density beyond a lifetime
-value is smaller than some percentage (default: 10%) of the maximum
-density.
+value is smaller than some ratio (see
+:ref:`kdeplot_density_ratio`) of the maximum density.
 
 The following plot is drawn with a
 19x19x19 mesh and nbins=200 and the ``Si-PBEsol`` example is used to
@@ -304,17 +304,20 @@ https://matplotlib.org/users/colormaps.html.
 
    % kdeplot --cmap="OrRd" kappa-m111111.hdf5
 
-``--min_density``
-^^^^^^^^^^^^^^^^^^
+.. _kdeplot_density_ratio:
+
+``--dr``, ``--density_ratio``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 **New** (``kdeplot`` is a stand-alone script. The latest version is
 download at
 https://github.com/atztogo/phono3py/blob/develop/scripts/kdeplot.)
 
 The density threshold is specified by the ratio with respect to
-maximum density. The default value is 0.1. When ``--ymax`` is
-specified together, this option is ignored.
+maximum density. Normally smaller value results in larger drawing
+region. The default value is 0.1. When ``--ymax`` is specified
+together, this option is ignored.
 
 ::
 
-   % kdeplot --min_density=0.01 kappa-m111111.hdf5
+   % kdeplot --dr=0.01 kappa-m111111.hdf5

scripts/kdeplot

@@ -35,7 +35,7 @@ def collect_data(gamma, weights, frequencies, t_index, cutoff, max_freq):
 
     return x, y
 
-def run_KDE(x, y, nbins, y_max=None, min_density=0.1):
+def run_KDE(x, y, nbins, y_max=None, density_ratio=0.1):
     """Running Gaussian-KDE by scipy
     """
 
@@ -59,7 +59,7 @@ def run_KDE(x, y, nbins, y_max=None, min_density=0.1):
         for i, r_zi in enumerate((zi.T)[::-1]):
             if indices:
                 indices.append(nbins - i - 1)
-            elif np.max(r_zi) > zi_max * min_density:
+            elif np.max(r_zi) > zi_max * density_ratio:
                 indices = [nbins - i - 1]
         short_nbinds = len(indices)
         
@@ -115,12 +115,12 @@ parser.add_argument("--cutoff",
                     help=("Property (y-axis) below this value is included in "
                           "data before running Gaussian-KDE"),
                     type=float, default=None)
-parser.add_argument("--fmax", help="Max frequency to plot",
-                    type=float, default=None)
-parser.add_argument("--min_density",
+parser.add_argument("--dr", "--density_ratio", dest="density_ratio",
                     help=("Minimum density ratio with respect to maximum "
                           "density used to determine drawing region"),
                     type=float, default=0.1)
+parser.add_argument("--fmax", help="Max frequency to plot",
+                    type=float, default=None)
 parser.add_argument('--nbins', type=int, default=100,
                     help=("Number of bins in which data are assigned, "
                           "i.e., determining resolution of plot")),
@@ -201,7 +201,7 @@ for gamma, s in zip(gammas, symbols):
                         t_index, args.cutoff, args.fmax)
     xi, yi, zi, short_nbinds = run_KDE(x, y, args.nbins,
                                        y_max=args.ymax,
-                                       min_density=args.min_density)
+                                       density_ratio=args.density_ratio)
     fig = plot(plt, xi, yi, zi, x, y, short_nbinds, args.nbins,
                y_max=args.ymax, cmap=args.cmap)
     if s: