def set_linewidth(self, w):
GraphicsContextBase.set_linewidth(self, w)
if w == 0:
self.gdkGC.line_width = 0
else:
pixels = self.renderer.points_to_pixels(w)
self.gdkGC.line_width = max(1, int(round(pixels)))
def set_linewidth(self, w):
"""
Set the line width.
"""
DEBUG_MSG("set_linewidth()", 1, self)
self.select()
if w>0 and w<1: w = 1
GraphicsContextBase.set_linewidth(self, w)
lw = int(self.renderer.points_to_pixels(self._linewidth))
if lw==0: lw = 1
self._pen.SetWidth(lw)
self.gfx_ctx.SetPen(self._pen)
self.unselect()
def set_linewidth(self, lw):
GraphicsContextBase.set_linewidth(self, lw)
pixels = self.renderer.points_to_pixels(lw)
if pixels<1: pixels = 1
else: pixels = round(pixels)
self.im.setThickness(pixels)
def set_linewidth(self, lw):
GraphicsContextBase.set_linewidth(self, lw)
pixels = self.renderer.points_to_pixels(lw)
if pixels < 1: pixels = 1
else: pixels = round(pixels)
self.im.setThickness(pixels)
def set_linewidth(self, w):
GraphicsContextBase.set_linewidth(self, w)
self.line['width'] = w
class MyPNG(PNG):
def __init__(self,
atoms,
rotation='',
show_unit_cell=False,
radii=None,
bbox=None,
colors=None,
model=None,
scale=20):
self.numbers = atoms.get_atomic_numbers()
self.colors = colors
self.model = model
if colors is None:
self.colors = jmol_colors[self.numbers]
if radii is None:
radii = covalent_radii[self.numbers]
elif type(radii) is float:
radii = covalent_radii[self.numbers] * radii
else:
radii = np.array(radii)
natoms = len(atoms)
if isinstance(rotation, str):
rotation = rotate(rotation)
A = atoms.get_cell()
if show_unit_cell > 0:
L, T, D = self.cell_to_lines(A)
C = np.empty((2, 2, 2, 3))
for c1 in range(2):
for c2 in range(2):
for c3 in range(2):
C[c1, c2, c3] = np.dot([c1, c2, c3], A)
C.shape = (8, 3)
C = np.dot(C, rotation) # Unit cell vertices
else:
L = np.empty((0, 3))
T = None
D = None
C = None
nlines = len(L)
X = np.empty((natoms + nlines, 3))
R = atoms.get_positions()
X[:natoms] = R
X[natoms:] = L
r2 = radii**2
for n in range(nlines):
d = D[T[n]]
if ((((R - L[n] - d)**2).sum(1) < r2) &
(((R - L[n] + d)**2).sum(1) < r2)).any():
T[n] = -1
X = np.dot(X, rotation)
R = X[:natoms]
if bbox is None:
X1 = (R - radii[:, None]).min(0)
X2 = (R + radii[:, None]).max(0)
if show_unit_cell == 2:
X1 = np.minimum(X1, C.min(0))
X2 = np.maximum(X2, C.max(0))
M = (X1 + X2) / 2
S = 1.05 * (X2 - X1)
w = scale * S[0]
#if w > 500:
#w = 500
#scale = w / S[0]
h = scale * S[1]
offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
else:
w = (bbox[2] - bbox[0]) * scale
h = (bbox[3] - bbox[1]) * scale
offset = np.array([bbox[0], bbox[1], 0]) * scale
self.w = w
self.h = h
X *= scale
X -= offset
if nlines > 0:
D = np.dot(D, rotation)[:, :2] * scale
if C is not None:
C *= scale
C -= offset
A = np.dot(A, rotation)
A *= scale
self.A = A
self.X = X
self.D = D
self.T = T
self.C = C
self.natoms = natoms
self.d = 2 * scale * radii
def write(self, filename, resolution=72):
self.filename = filename
self.write_header(resolution=resolution)
self.write_info()
self.write_body()
self.write_trailer(resolution=resolution)
def write_info(self):
def latex_float(f):
float_str = "{0:.2e}".format(f)
if "e" in float_str:
base, exponent = float_str.split("e")
return r"{0} \times 10^{{{1}}}".format(base, int(exponent))
else:
return float_str
import matplotlib.text
if self.model is not None:
time = latex_float(self.model.base.get_kmc_time())
text = matplotlib.text.Text(
.05 * self.w,
.9 * self.h,
r'$t = {time}\,{{\rm s}}$'.format(**locals()),
fontsize=36,
bbox={
'facecolor': 'white',
'alpha': 0.5,
'ec': 'white',
'pad': 1,
'lw': 0
},
)
text.figure = self.figure
text.draw(self.renderer)
def write_header(self, resolution=72):
from matplotlib.backends.backend_agg import RendererAgg, Figure
from matplotlib.backend_bases import GraphicsContextBase
try:
from matplotlib.transforms import Value
except ImportError:
dpi = resolution
else:
dpi = Value(resolution)
self.renderer = RendererAgg(self.w, self.h, dpi)
self.figure = Figure()
self.gc = GraphicsContextBase()
self.gc.set_linewidth(.2)
def write_trailer(self, resolution=72):
renderer = self.renderer
if hasattr(renderer._renderer, 'write_png'):
# Old version of matplotlib:
renderer._renderer.write_png(self.filename)
else:
from matplotlib import _png
# buffer_rgba does not accept arguments from version 1.2.0
# https://github.com/matplotlib/matplotlib/commit/f4fee350f9fbc639853bee76472d8089a10b40bd
import matplotlib
if matplotlib.__version__ < '1.2.0':
x = renderer._renderer.buffer_rgba(0, 0)
_png.write_png(renderer._renderer.buffer_rgba(0, 0),
renderer.width, renderer.height, self.filename,
resolution)
else:
x = renderer._renderer.buffer_rgba()
_png.write_png(
renderer._renderer.buffer_rgba(),
#renderer.width, renderer.height,
self.filename,
resolution)
class MyPNG(PNG):
def __init__(self, atoms,
rotation='',
show_unit_cell=False,
radii=None,
bbox=None,
colors=None,
model=None,
scale=20) :
self.numbers = atoms.get_atomic_numbers()
self.colors = colors
self.model = model
if colors is None:
self.colors = jmol_colors[self.numbers]
if radii is None:
radii = covalent_radii[self.numbers]
elif type(radii) is float:
radii = covalent_radii[self.numbers] * radii
else:
radii = np.array(radii)
natoms = len(atoms)
if isinstance(rotation, str):
rotation = rotate(rotation)
A = atoms.get_cell()
if show_unit_cell > 0:
L, T, D = self.cell_to_lines(A)
C = np.empty((2, 2, 2, 3))
for c1 in range(2):
for c2 in range(2):
for c3 in range(2):
C[c1, c2, c3] = np.dot([c1, c2, c3], A)
C.shape = (8, 3)
C = np.dot(C, rotation) # Unit cell vertices
else:
L = np.empty((0, 3))
T = None
D = None
C = None
nlines = len(L)
X = np.empty((natoms + nlines, 3))
R = atoms.get_positions()
X[:natoms] = R
X[natoms:] = L
r2 = radii**2
for n in range(nlines):
d = D[T[n]]
if ((((R - L[n] - d)**2).sum(1) < r2) &
(((R - L[n] + d)**2).sum(1) < r2)).any():
T[n] = -1
X = np.dot(X, rotation)
R = X[:natoms]
if bbox is None:
X1 = (R - radii[:, None]).min(0)
X2 = (R + radii[:, None]).max(0)
if show_unit_cell == 2:
X1 = np.minimum(X1, C.min(0))
X2 = np.maximum(X2, C.max(0))
M = (X1 + X2) / 2
S = 1.05 * (X2 - X1)
w = scale * S[0]
#if w > 500:
#w = 500
#scale = w / S[0]
h = scale * S[1]
offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
else:
w = (bbox[2] - bbox[0]) * scale
h = (bbox[3] - bbox[1]) * scale
offset = np.array([bbox[0], bbox[1], 0]) * scale
self.w = w
self.h = h
X *= scale
X -= offset
if nlines > 0:
D = np.dot(D, rotation)[:, :2] * scale
if C is not None:
C *= scale
C -= offset
A = np.dot(A, rotation)
A *= scale
self.A = A
self.X = X
self.D = D
self.T = T
self.C = C
self.natoms = natoms
self.d = 2 * scale * radii
def write(self, filename, resolution=72):
self.filename = filename
self.write_header(resolution=resolution)
self.write_info()
self.write_body()
self.write_trailer(resolution=resolution)
def write_info(self):
def latex_float(f):
float_str = "{0:.2e}".format(f)
if "e" in float_str:
base, exponent = float_str.split("e")
return r"{0} \times 10^{{{1}}}".format(base, int(exponent))
else:
return float_str
import matplotlib.text
if self.model is not None:
time = latex_float(self.model.base.get_kmc_time())
text = matplotlib.text.Text(.05*self.w,
.9*self.h,
r'$t = {time}\,{{\rm s}}$'.format(**locals()),
fontsize=36,
bbox={'facecolor':'white', 'alpha':0.5, 'ec':'white', 'pad':1, 'lw':0 },
)
text.figure = self.figure
text.draw(self.renderer)
def write_header(self, resolution=72):
from matplotlib.backends.backend_agg import RendererAgg, Figure
from matplotlib.backend_bases import GraphicsContextBase
try:
from matplotlib.transforms import Value
except ImportError:
dpi = resolution
else:
dpi = Value(resolution)
self.renderer = RendererAgg(self.w, self.h, dpi)
self.figure = Figure()
self.gc = GraphicsContextBase()
self.gc.set_linewidth(.2)
def write_trailer(self, resolution=72):
renderer = self.renderer
if hasattr(renderer._renderer, 'write_png'):
# Old version of matplotlib:
renderer._renderer.write_png(self.filename)
else:
from matplotlib import _png
# buffer_rgba does not accept arguments from version 1.2.0
# https://github.com/matplotlib/matplotlib/commit/f4fee350f9fbc639853bee76472d8089a10b40bd
import matplotlib
if matplotlib.__version__ < '1.2.0':
x = renderer._renderer.buffer_rgba(0, 0)
_png.write_png(renderer._renderer.buffer_rgba(0, 0),
renderer.width, renderer.height,
self.filename, resolution)
else:
x = renderer._renderer.buffer_rgba()
_png.write_png(renderer._renderer.buffer_rgba(),
renderer.width, renderer.height,
self.filename, resolution)
def set_linewidth(self, w):
GraphicsContextBase.set_linewidth(self, w)
self.line['width'] = w
def set_linewidth(self, lw):
GraphicsContextBase.set_linewidth(self, lw)
pixels = self.renderer.points_to_pixels(lw)
self.gdkGC.line_width = max(1, int(round(pixels)))