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--xmax is implemented for kdeplot.

This commit is contained in:
Atsushi Togo 2017-06-10 18:51:06 +02:00
parent 42251d5eb4
commit 5835dcef93
2 changed files with 25 additions and 14 deletions
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24
doc/auxiliary-tools.rst
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@ -277,12 +277,19 @@ Gaussian-KDE. Normally increasing this value from the chosen value
without specifying this option does nothing since automatic control of
drawing area cuts high lifetime (frequency) side if the density is low.
``--ymax``
^^^^^^^^^^^
``--xmax`` and ``--ymax``
^^^^^^^^^^^^^^^^^^^^^^^^^^
Maximum value of drawing region of lifetime (y) axis. This switches
off automatic determination of drawing area, therefore as a side
effect, the computation will be roughly twice faster.
**New**: The latest version of ``kdeplot`` is download at
https://github.com/atztogo/phono3py/blob/develop/scripts/kdeplot.)
Maximum values of drawing region of phonon frequency (x-axis) and
lifetime (y-axis) are specified by ``--xmax`` and ``--ymax``,
respectively.
``--ymax`` switches off automatic determination of maximum value
of drawing region along y-axis, therefore as a side effect, the
computation will be roughly twice faster.
::
@ -291,11 +298,9 @@ effect, the computation will be roughly twice faster.
``--cmap``
^^^^^^^^^^^
**New** (``kdeplot`` is a stand-alone script. The latest version is
download at
**New**: The latest version of ``kdeplot`` is download at
https://github.com/atztogo/phono3py/blob/develop/scripts/kdeplot.)
Color map to be used for the density plot. It's given by the name
presented at the matplotlib documentation,
https://matplotlib.org/users/colormaps.html.
@ -309,8 +314,7 @@ https://matplotlib.org/users/colormaps.html.
``--dr``, ``--density_ratio``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**New** (``kdeplot`` is a stand-alone script. The latest version is
download at
**New**: The latest version of ``kdeplot`` is download at
https://github.com/atztogo/phono3py/blob/develop/scripts/kdeplot.)
The density threshold is specified by the ratio with respect to

15
scripts/kdeplot
View File

@ -35,12 +35,15 @@ def collect_data(gamma, weights, frequencies, t_index, cutoff, max_freq):
return x, y
def run_KDE(x, y, nbins, y_max=None, density_ratio=0.1):
def run_KDE(x, y, nbins, x_max=None, y_max=None, density_ratio=0.1):
"""Running Gaussian-KDE by scipy
"""
x_min = 0
x_max = np.rint(x.max() * 1.1)
if x_max is None:
_x_max = np.rint(x.max() * 1.1)
else:
_x_max = x_max
y_min = 0
if y_max is None:
_y_max = np.rint(y.max())
@ -49,7 +52,7 @@ def run_KDE(x, y, nbins, y_max=None, density_ratio=0.1):
values = np.vstack([x.ravel(), y.ravel()])
kernel = stats.gaussian_kde(values)
xi, yi = np.mgrid[x_min:x_max:nbins*1j, y_min:_y_max:nbins*1j]
xi, yi = np.mgrid[x_min:_x_max:nbins*1j, y_min:_y_max:nbins*1j]
positions = np.vstack([xi.ravel(), yi.ravel()])
zi = np.reshape(kernel(positions).T, xi.shape)
@ -64,7 +67,7 @@ def run_KDE(x, y, nbins, y_max=None, density_ratio=0.1):
short_nbinds = len(indices)
ynbins = nbins ** 2 // short_nbinds
xi, yi = np.mgrid[x_min:x_max:nbins*1j, y_min:_y_max:ynbins*1j]
xi, yi = np.mgrid[x_min:_x_max:nbins*1j, y_min:_y_max:ynbins*1j]
positions = np.vstack([xi.ravel(), yi.ravel()])
zi = np.reshape(kernel(positions).T, xi.shape)
else:
@ -129,6 +132,9 @@ parser.add_argument('--temperature', type=float, default=300.0,
dest='temperature',
help='Temperature to output data at')
parser.add_argument("--title", dest="title", default=None, help="Plot title")
parser.add_argument("--xmax",
help="Set maximum x of draw area",
type=float, default=None)
parser.add_argument("--ymax",
help="Set maximum y of draw area",
type=float, default=None)
@ -200,6 +206,7 @@ for gamma, s in zip(gammas, symbols):
x, y = collect_data(gamma, weights, frequencies,
t_index, args.cutoff, args.fmax)
xi, yi, zi, short_nbinds = run_KDE(x, y, args.nbins,
x_max=args.xmax,
y_max=args.ymax,
density_ratio=args.density_ratio)
fig = plot(plt, xi, yi, zi, x, y, short_nbinds, args.nbins,