def render(self, ax):
from matplotlib import pyplot
from matplotlib import colors
render_2d.render(self, ax)
if self._open_circle_points.size():
x, y = self._open_circle_points.parts()
ax.scatter(
x.as_numpy_array(), y.as_numpy_array(), s=self._open_circle_radii,
marker='o', edgecolors=self._open_circle_colors, facecolors=None)
if self._filled_circle_points.size():
x, y = self._filled_circle_points.parts()
# use pyplot colormaps then we can more easily get a colorbar
data = self.scene.multiplicities.data()
cmap_d = {
'heatmap': 'hot',
'redblue': colors.LinearSegmentedColormap.from_list("RedBlud",["b","r"]),
'grayscale': 'Greys_r' if self.settings.black_background else 'Greys',
'mono': (colors.LinearSegmentedColormap.from_list("mono",["w","w"])
if self.settings.black_background
else colors.LinearSegmentedColormap.from_list("mono",["black","black"])),
}
cm = cmap_d.get(
self.settings.color_scheme, self.settings.color_scheme)
if isinstance(cm, basestring):
cm = pyplot.cm.get_cmap(cm)
im = ax.scatter(
x.as_numpy_array(), y.as_numpy_array(), s=self._filled_circle_radii,
marker='o',
c=data.select(self.scene.slice_selection).as_numpy_array(),
edgecolors='none',
vmin=0, vmax=flex.max(data),
cmap=cm)
# colorbar
cb = self.fig.colorbar(im, ax=ax)
[t.set_color(self._foreground) for t in cb.ax.get_yticklabels()]
[t.set_fontsize(self.settings.font_size) for t in cb.ax.get_yticklabels()]
self.ax.set_aspect('equal')
self.ax.set_axis_bgcolor(self._background)
xmax, ymax = self.GetSize()
ax.set_xlim(0, xmax)
ax.set_ylim(0, ymax)
ax.invert_yaxis()
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
self.fig.tight_layout()
self.fig.savefig(
self.settings.filename, bbox_inches='tight', facecolor=self._background)
def render(self, ax):
from matplotlib import pyplot
from matplotlib import colors
render_2d.render(self, ax)
if self._open_circle_points.size():
x, y = self._open_circle_points.parts()
ax.scatter(
x.as_numpy_array(),
y.as_numpy_array(),
s=self._open_circle_radii,
marker="o",
edgecolors=self._open_circle_colors,
facecolors=None,
)
if self._filled_circle_points.size():
x, y = self._filled_circle_points.parts()
# use pyplot colormaps then we can more easily get a colorbar
data = self.scene.multiplicities.data()
cmap_d = {
"heatmap": "hot",
"redblue": colors.LinearSegmentedColormap.from_list(
"RedBlue", ["b", "r"]
),
"grayscale": "Greys_r" if self.settings.black_background else "Greys",
"mono": (
colors.LinearSegmentedColormap.from_list("mono", ["w", "w"])
if self.settings.black_background
else colors.LinearSegmentedColormap.from_list(
"mono", ["black", "black"]
)
),
}
cm = cmap_d.get(self.settings.color_scheme, self.settings.color_scheme)
if isinstance(cm, str):
cm = pyplot.cm.get_cmap(cm)
im = ax.scatter(
x.as_numpy_array(),
y.as_numpy_array(),
s=self._filled_circle_radii,
marker="o",
c=data.select(self.scene.slice_selection).as_numpy_array(),
edgecolors="none",
vmin=0,
vmax=flex.max(data),
cmap=cm,
)
# colorbar
cb = self.fig.colorbar(im, ax=ax)
[t.set_color(self._foreground) for t in cb.ax.get_yticklabels()]
[t.set_fontsize(self.settings.font_size) for t in cb.ax.get_yticklabels()]
self.ax.set_aspect("equal")
self.ax.set_facecolor(self._background)
xmax, ymax = self.GetSize()
ax.set_xlim(0, xmax)
ax.set_ylim(0, ymax)
ax.invert_yaxis()
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
self.fig.tight_layout()
self.fig.savefig(
self.settings.plot.filename, bbox_inches="tight", facecolor=self._background
)
def render(self, ax):
render_2d.render(self, ax)
data = []
if self._open_circle_points.size():
x, y = self._open_circle_points.parts()
z = self._open_circle_colors
data.append(
{
"x": list(x.round(1)),
"y": list(y.round(1)),
#'z': list(z),
"type": "scatter",
"mode": "markers",
"name": "missing reflections",
"showlegend": False,
"marker": {
#'color': list(z),
"color": (
"white" if self.settings.black_background else "black"
),
"line": {
#'color': 'black',
"width": 0
},
"symbol": "circle",
"size": 5,
},
}
)
if self._filled_circle_points.size():
x, y = self._filled_circle_points.parts()
z = self.scene.multiplicities.data().select(self.scene.slice_selection)
# why doesn't this work?
# colorscale = []
# assert len(z) == len(self._filled_circle_colors)
# for zi in range(flex.max(z)+1):
# i = flex.first_index(z, zi)
# if i is None: continue
# print i, self._filled_circle_colors[i], 'rgb(%i,%i,%i)' %tuple(rgb * 264 for rgb in self._filled_circle_colors[i])
# colorscale.append([zi, 'rgb(%i,%i,%i)' %self._filled_circle_colors[i]])
cmap_d = {
"rainbow": "Jet",
"heatmap": "Hot",
"redblue": "RdbU",
"grayscale": "Greys",
"mono": None,
}
color = list(z)
colorscale = cmap_d.get(
self.settings.color_scheme, self.settings.color_scheme
)
if self.settings.color_scheme == "mono":
color = "black"
colorscale = None
data.append(
{
"x": list(x.round(1)),
"y": list(y.round(1)),
#'z': list(z),
"type": "scatter",
"mode": "markers",
"name": "multiplicity",
"showlegend": False,
"marker": {
"color": color,
"colorscale": colorscale,
"cmin": 0,
"cmax": flex.max(self.scene.multiplicities.data()),
"showscale": True,
"colorbar": {"title": "Multiplicity", "titleside": "right"},
"line": {
#'color': 'white',
"width": 0
},
"symbol": "circle",
"size": 5,
},
}
)
text = {"mode": "text", "showlegend": False, "textposition": "top right"}
text.update(self._text)
data.append(text)
shapes = []
for x0, y0, x1, y1 in self._lines:
# color = 'rgb(%i,%i,%i)' %tuple(rgb * 264 for rgb in self._foreground)
color = "black"
shapes.append(
{
"type": "line",
"x0": x0,
"y0": y0,
"x1": x1,
"y1": y1,
"layer": "below",
"line": {"color": color, "width": 2},
}
)
d = {
"data": data,
"layout": {
"plot_bgcolor": "rgb(%i,%i,%i)"
% tuple(rgb * 264 for rgb in self._background),
"title": "Multiplicity plot (%s=%s)"
% (self.settings.slice_axis, self.settings.slice_index),
"shapes": shapes,
"hovermode": False,
"xaxis": {
"showgrid": False,
"zeroline": False,
"showline": False,
"ticks": "",
"showticklabels": False,
},
"yaxis": {
"autorange": "reversed",
"showgrid": False,
"zeroline": False,
"showline": False,
"ticks": "",
"showticklabels": False,
},
},
}
return d
def render(self, ax):
render_2d.render(self, ax)
data = []
if self._open_circle_points.size():
x, y = self._open_circle_points.parts()
z = self._open_circle_colors
data.append({
'x': list(x.round(1)),
'y': list(y.round(1)),
#'z': list(z),
'type': 'scatter',
'mode': 'markers',
'name': 'missing reflections',
'showlegend': False,
'marker': {
#'color': list(z),
'color':
('white' if self.settings.black_background else 'black'),
'line': {
#'color': 'black',
'width': 0,
},
'symbol':
'circle',
'size':
5,
},
})
if self._filled_circle_points.size():
x, y = self._filled_circle_points.parts()
z = self.scene.multiplicities.data().select(
self.scene.slice_selection)
# why doesn't this work?
#colorscale = []
#assert len(z) == len(self._filled_circle_colors)
#for zi in range(flex.max(z)+1):
# i = flex.first_index(z, zi)
# if i is None: continue
# print i, self._filled_circle_colors[i], 'rgb(%i,%i,%i)' %tuple(rgb * 264 for rgb in self._filled_circle_colors[i])
# colorscale.append([zi, 'rgb(%i,%i,%i)' %self._filled_circle_colors[i]])
cmap_d = {
'rainbow': 'Jet',
'heatmap': 'Hot',
'redblue': 'RdbU',
'grayscale': 'Greys',
'mono': None,
}
color = list(z)
colorscale = cmap_d.get(self.settings.color_scheme,
self.settings.color_scheme)
if self.settings.color_scheme == 'mono':
color = 'black'
colorscale = None
data.append({
'x': list(x.round(1)),
'y': list(y.round(1)),
#'z': list(z),
'type': 'scatter',
'mode': 'markers',
'name': 'multiplicity',
'showlegend': False,
'marker': {
'color': color,
'colorscale': colorscale,
'cmin': 0,
'cmax': flex.max(self.scene.multiplicities.data()),
'showscale': True,
'colorbar': {
'title': 'Multiplicity',
'titleside': 'right',
},
'line': {
#'color': 'white',
'width': 0,
},
'symbol': 'circle',
'size': 5,
},
})
text = {
'x': [x for x, y, text in self._text],
'y': [y for x, y, text in self._text],
'text': [text for x, y, text in self._text],
'mode': 'text',
'showlegend': False,
'textposition': 'top right',
}
data.append(text)
shapes = []
for x0, y0, x1, y1 in self._lines:
#color = 'rgb(%i,%i,%i)' %tuple(rgb * 264 for rgb in self._foreground)
color = 'black'
shapes.append({
'type': 'line',
'x0': x0,
'y0': y0,
'x1': x1,
'y1': y1,
'layer': 'below',
'line': {
'color': color,
'width': 2,
}
})
d = {
'data': data,
'layout': {
'plot_bgcolor':
'rgb(%i,%i,%i)' % tuple(rgb * 264 for rgb in self._background),
'title':
'Multiplicity plot (%s=%s)' %
(self.settings.slice_axis, self.settings.slice_index),
'shapes':
shapes,
'hovermode':
False,
'xaxis': {
'showgrid': False,
'zeroline': False,
'showline': False,
'ticks': '',
'showticklabels': False,
},
'yaxis': {
'autorange': 'reversed',
'showgrid': False,
'zeroline': False,
'showline': False,
'ticks': '',
'showticklabels': False,
},
},
}
return d