def demo_fixed_pad_axes():
fig = plt.figure(2, (6, 6))
# The first & third items are for padding and the second items are for the axes.
# sizes are in inch.
h = [
Size.Fixed(1.0),
Size.Scaled(1.),
Size.Fixed(.2),
]
v = [
Size.Fixed(0.7),
Size.Scaled(1.),
Size.Fixed(.5),
]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
# the width and height of the rectangle is ignored.
ax = LocatableAxes(fig, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(ax)
ax.plot([1, 2, 3])
def metric_svg(self,
host=None,
title="undefined",
ylabel="undefined",
metrics=[],
b64encode=True):
fig = pyplot.figure(figsize=self.FIGSIZE)
h = [Size.Fixed(1.2), Size.Scaled(1.), Size.Fixed(.2)]
v = [Size.Fixed(0.7), Size.Scaled(1.), Size.Fixed(.5)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
plt = Axes(fig, divider.get_position())
plt.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(plt)
result = self.result
runinfo = result.runinfo
# ----
# The X limits are -rampupMins, runMins
# ----
plt.set_xlim(-int(runinfo['rampupMins']), int(runinfo['runMins']))
plt.axvspan(-int(runinfo['rampupMins']), 0, facecolor='0.2', alpha=0.1)
# ----
# Draw all the requested graphs
# ----
x = None
for m in metrics:
if x is None:
x, y = self._get_metric_tree(m)
else:
_, y = self._get_metric_tree(m, x)
plt.plot(x, y, m['color'], label=m['label'])
# ----
# Title and labels
# ----
plt.set_title(title)
plt.set_xlabel("Elapsed Minutes")
plt.set_ylabel(ylabel)
plt.legend(loc='upper left')
plt.grid()
# ----
# Now turn this into an in-memory SVG and return it as requested
# (raw or b64-encoded)
# ----
buf = io.StringIO()
pyplot.savefig(buf, format='svg')
if not b64encode:
return buf.getvalue()
return base64.b64encode(buf.getvalue().encode('utf-8')).decode('utf-8')
def plot_it():
# fig = plt.figure(1, figsize=(8, 4.5))
fig = plt.figure(1, figsize=(16, 12))
# h = [Size.Fixed(0.), Size.Fixed(6.5)]
# v = [Size.Fixed(0.5), Size.Fixed(3.25)]
h = [Size.Fixed(0.), Size.Fixed(13)]
v = [Size.Fixed(0.5), Size.Fixed(7)]
win = Divider(fig, (0.1, 0.08, 0.8, 0.8), h, v, aspect=False)
ax = Axes(fig, win.get_position())
ax.set_axes_locator(win.new_locator(nx=1, ny=1))
fig.add_axes(ax)
# fig = plt.figure(figsize=(16, 12))
# ax = fig.add_subplot(111)
for ii, ellipse in enumerate(ellipses):
ax.fill(ellipse[0], ellipse[1], color=cmap(norm_vals[ii]), zorder=0)
ax.plot(ellipse[0], ellipse[1], 'k-', linewidth=0.2)
ax.invert_yaxis()
plt.xlabel('Northing (km)', fontsize=16)
plt.ylabel(r'$\log_{10}$ Period (s)', fontsize=16)
# ax.set_aspect(1)
ax.tick_params(axis='both', labelsize=14)
# locs, labels = plt.xticks()
# plt.xticks(locs, [int(x * 10) for x in locs])
fake_vals = np.linspace(lower, upper, len(fill_vals))
fake_im = ax.scatter(loc, periods, c=fake_vals, cmap=cmap)
fake_im.set_visible(False)
# ax.set_ylim([-2.6, 3.25])
# ax.set_xlim([526.5, 538.2])
# ax.invert_yaxis()
# cb = plt.colorbar(mappable=fake_im)
#############################################
# Colour bar and site labelling
# cbaxes = fig.add_axes([0.925, 0.1351, 0.015, 0.72])
# cb = plt.colorbar(fake_im)
# if 'phi' in fill_param[:3]:
# label = r'${}{}(\degree)$'.format('\phi', fill_param[-2:])
# else:
# label = r'$\{}(\degree)$'.format(fill_param)
# cb.set_label(label,
# rotation=270,
# labelpad=20,
# fontsize=18)
# ax.tick_params(axis='both', labelsize=14)
# ax.set_xlim(x_lim)
# for ii, site in enumerate(main_sites):
# txt = site[-4:-1]
# if linear_xaxis:
# ax.text(linear_site[ii],
# label_offset, site, rotation=45) # 3.6
# else:
# ax.text(main_transect.sites[site].locations['X'],
# label_offset, site, rotation=45) # 3.6
plt.show()
return fig
def _set_ax_height_to_cm(fig: Fig, ax: Ax, height: float) -> None:
from mpl_toolkits.axes_grid1 import Size, Divider
height /= 2.54 # cm to inches
bbox = _get_ax_bbox(fig, ax)
hori = [Size.Fixed(bbox.x0), Size.Fixed(bbox.width), Size.Fixed(bbox.x1)]
vert = [Size.Fixed(bbox.y0), Size.Fixed(height), Size.Fixed(bbox.y1)]
divider = Divider(fig, (0.0, 0.0, 1.0, 1.0), hori, vert, aspect=False)
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
def demo_fixed_pad_axes():
fig = plt.figure(2, (6, 6))
# The first & third items are for padding and the second items are for the
# axes. Sizes are in inches.
h = [Size.Fixed(1.0), Size.Scaled(1.), Size.Fixed(.2)]
v = [Size.Fixed(0.7), Size.Scaled(1.), Size.Fixed(.5)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
# the width and height of the rectangle is ignored.
ax = LocatableAxes(fig, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(ax)
ax.plot([1, 2, 3])
def demo_fixed_size_axes():
fig = plt.figure(figsize=(6, 6))
# The first items are for padding and the second items are for the axes.
# sizes are in inch.
h = [Size.Fixed(1.0), Size.Fixed(4.5)]
v = [Size.Fixed(0.7), Size.Fixed(5.)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
# the width and height of the rectangle is ignored.
ax = Axes(fig, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(ax)
ax.plot([1, 2, 3])
def demo_fixed_size_axes():
fig1 = plt.figure(1, (10, 5))
# The first items are for padding and the second items are for the axes.
# sizes are in inch.
h = [Size.Fixed(1.0), Size.Fixed(7.5)]
v = [Size.Fixed(0.7), Size.Fixed(4.5)]
divider = Divider(fig1, (0.0, 0.0, 1., 1.), h, v, aspect=False)
# the width and height of the rectangle is ignored.
ax = LocatableAxes(fig1, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig1.add_axes(ax)
ax.plot([1, 2, 3])
def fig(self):
fig, axes = plt.subplots(nrows=self.nrows, ncols=self.ncols, figsize=self.figsize)
divider = Divider(fig, (0.0, 0.0, 1.0, 1.0), self.h, self.v, aspect=False)
if (self.nrows == 1) & (self.ncols == 1):
axes = [axes]
axes[0].set_axes_locator(divider.new_locator(nx=1, ny=1))
if self.n_axes > 1:
for i in range(self.n_axes-1):
axes.append(fig.add_subplot(111))
axes[i+1].set_axes_locator(divider.new_locator(nx=1, ny=1))
elif self.nrows > 1:
for j in range(self.nrows):
axes[j].set_axes_locator(divider.new_locator(nx=1, ny=j*2+1))
elif self.ncols > 1:
for i in range(self.ncols):
axes[i].set_axes_locator(divider.new_locator(nx=i*2+1, ny=1))
if (self.nrows > 1) & (self.ncols > 1):
for j in range(self.nrows):
for i in range(self.ncols):
axes[i, j].set_axes_locator(divider.new_locator(nx=i*2+1, ny=j*2+1))
return fig, axes
def fix_sz_fig(width, height, width_ext=2, padding=.5):
# These code is to make fixed size article
# Makesure matplotlib can draw Chinese characters
plt.rcParams['font.sans-serif'] = ['SimHei']
# Init figure
fig = plt.figure(figsize=(width + 2 * padding + width_ext,
height + 2 * padding))
# The first items are for padding and the second items are for the axes.
# Article width and height
w = [Size.Fixed(padding), Size.Fixed(width)]
h = [Size.Fixed(padding), Size.Fixed(height)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), w, h, aspect=False)
# the width and height of the rectangle is ignored.
ax = Axes(fig, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(ax)
return fig, ax
def create_plot(two_sided=False,
colors=[
'#6F4C9B', '#5568B8', '#4D8AC6', '#60AB9E', '#77B77D',
'#A6BE54', '#D1B541', '#E49C39', '#DF4828', '#990D38'
],
markers=['o', 'v', '^', 's', 'D', '*'],
figsize=(5, 3.4)):
"""
Crée un environnement de plot
Parameters
----------
twosided : bool
allows to change the size of the figure accordingly.
colors : list of strings
a default list exists but this allows to change it if u want
markers : list of strings
a default list of markers exists, but u can change it if needed
Returns
-------
fig, ax : matplotlib objects to be used as normal
"""
color = cycle(colors)
marker = cycle(markers)
if two_sided:
fig = plt.figure(figsize=(3.4, 3.4))
else:
fig = plt.figure(figsize=figsize)
# The first & third items are for padding and the second items are for the
# axes. Sizes are in inches.
h = [Size.Fixed(1.0), Size.Scaled(1.), Size.Fixed(.2)]
v = [Size.Fixed(0.7), Size.Scaled(1.), Size.Fixed(.5)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
# the width and height of the rectangle is ignored.
ax = Axes(fig, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(ax)
return fig, ax, color, marker
def set_size3(ax, w, h):
# https://newbedev.com/axes-class-set-explicitly-size-width-height-of-axes-in-given-units
from mpl_toolkits.axes_grid1 import Divider, Size
axew = w / 2.54
axeh = h / 2.54
# lets use the tight layout function to get a good padding size for our axes labels.
# fig = plt.gcf()
# ax = plt.gca()
fig = ax.get_figure()
fig.tight_layout()
# obtain the current ratio values for padding and fix size
oldw, oldh = fig.get_size_inches()
l = ax.figure.subplotpars.left
r = ax.figure.subplotpars.right
t = ax.figure.subplotpars.top
b = ax.figure.subplotpars.bottom
# work out what the new ratio values for padding are, and the new fig size.
# ps: adding a bit to neww and newh gives more padding
# the axis size is set from axew and axeh
neww = axew + oldw * (1 - r + l) + 0.4
newh = axeh + oldh * (1 - t + b) + 0.4
newr = r * oldw / neww - 0.4
newl = l * oldw / neww + 0.4
newt = t * oldh / newh - 0.4
newb = b * oldh / newh + 0.4
# right(top) padding, fixed axes size, left(bottom) pading
hori = [Size.Scaled(newr), Size.Fixed(axew), Size.Scaled(newl)]
vert = [Size.Scaled(newt), Size.Fixed(axeh), Size.Scaled(newb)]
divider = Divider(fig, (0.0, 0.0, 1.0, 1.0), hori, vert, aspect=False)
# the width and height of the rectangle is ignored.
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
# we need to resize the figure now, as we have may have made our axes bigger than in.
fig.set_size_inches(neww, newh)
def subplot_array(self, hsize, vsize=(1.0, ), figsize=(10, 10)):
""" Use the axes_divider module to make a single row of plots
hsize : list of floats
horizontal spacing: alternates Scaled for plot, Fixed for between plots
vsize : list of floats
vertical spacing
ref: http://matplotlib.org/mpl_toolkits/axes_grid/users/axes_divider.html
"""
nx = (len(hsize) + 1) / 2
ny = (len(vsize) + 1) / 2
fig, axx = plt.subplots(
ny, nx, squeeze=False,
figsize=figsize) # just to make the axes, will move them
sizer = lambda x, i: axes_size.Scaled(
x) if i % 2 == 0 else axes_size.Fixed(x)
horiz = [sizer(h, i) for i, h in enumerate(hsize)]
vert = [sizer(v, i) for i, v in enumerate(vsize)]
divider = Divider(fig, (0.1, 0.1, 0.8, 0.8), horiz, vert, aspect=False)
for i, ax in enumerate(axx.flatten()):
iy = i // nx
ix = i % nx
ax.set_axes_locator(divider.new_locator(nx=2 * ix, ny=2 * iy))
return fig, axx
def get_divider(self, fig):
self.border = 0.1
while self.actual_size[0] < (
self.size_on_screen[0] - 2 * self.border
) and self.actual_size[1] < (self.size_on_screen[1] - 2 * self.border):
self.border += 0.1
x_factor = self.actual_size[0] / (self.size_on_screen[0] -
2 * self.border)
y_factor = self.actual_size[1] / (self.size_on_screen[1] -
2 * self.border)
self.scale = max(x_factor, y_factor)
draw_size = (self.actual_size[0] / self.scale,
self.actual_size[1] / self.scale)
h = [Size.Fixed(self.border), Size.Fixed(draw_size[0])]
v = [Size.Fixed(self.border), Size.Fixed(draw_size[1])]
return Divider(
fig,
(self.location_on_screen[0], self.location_on_screen[1], 1, 1),
h,
v,
aspect=False)
def __init__(self,
ax_size,
wspace,
dpi,
cbar,
cbar_width,
left,
bottom,
right,
top,
fig_func=None):
if not cbar:
wspace = 0
cbar_width = 0
# convert arguments from pixels to inches
ax_size = np.asarray(ax_size) / dpi
wspace, cbar_width, left, bottom, right, top = np.array(
(wspace, cbar_width, left, bottom, right, top)) / dpi
horiz = [left, ax_size[0], wspace, cbar_width, right]
vert = [bottom, ax_size[1], top]
figsize = (sum(horiz), sum(vert))
fig_func = plt.figure if fig_func is None else fig_func
fig = fig_func(figsize=figsize, dpi=dpi)
horiz, vert = list(map(Size.Fixed, horiz)), list(map(Size.Fixed, vert))
divider = Divider(fig, (0.0, 0.0, 1., 1.), horiz, vert, aspect=False)
ax = LocatableAxes(fig, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(ax)
if cbar:
cax = LocatableAxes(fig, divider.get_position())
cax.set_axes_locator(divider.new_locator(nx=3, ny=1))
fig.add_axes(cax)
self.fig = fig
self.ax = ax
self.cax = cax if cbar else None
os.remove(temppath)
size(W, HEIGHT+dy+40)
else:
def pltshow(mplpyplot):
mplpyplot.show()
# nodebox section end
fig1 = plt.figure(1, (5.5, 4.))
# the rect parameter will be ignore as we will set axes_locator
rect = (0.1, 0.1, 0.8, 0.8)
ax = [fig1.add_axes(rect, label="%d" % i) for i in range(4)]
horiz = [Size.Scaled(1.5), Size.Fixed(.5), Size.Scaled(1.),
Size.Scaled(.5)]
vert = [Size.Scaled(1.), Size.Fixed(.5), Size.Scaled(1.5)]
# divide the axes rectangle into grid whose size is specified by horiz * vert
divider = Divider(fig1, rect, horiz, vert, aspect=False)
ax[0].set_axes_locator(divider.new_locator(nx=0, ny=0))
ax[1].set_axes_locator(divider.new_locator(nx=0, ny=2))
ax[2].set_axes_locator(divider.new_locator(nx=2, ny=2))
ax[3].set_axes_locator(divider.new_locator(nx=2, nx1=4, ny=0))
for ax1 in ax:
ax1.tick_params(labelbottom=False, labelleft=False)
pltshow(plt)
from mpl_toolkits.axes_grid1 import Divider import matplotlib.pyplot as plt fig = plt.figure(figsize=(5.5, 4)) # the rect parameter will be ignore as we will set axes_locator rect = (0.1, 0.1, 0.8, 0.8) ax = [fig.add_axes(rect, label="%d" % i) for i in range(4)] horiz = [Size.AxesX(ax[0]), Size.Fixed(.5), Size.AxesX(ax[1])] vert = [Size.AxesY(ax[0]), Size.Fixed(.5), Size.AxesY(ax[2])] # divide the axes rectangle into grid whose size is specified by horiz * vert divider = Divider(fig, rect, horiz, vert, aspect=False) ax[0].set_axes_locator(divider.new_locator(nx=0, ny=0)) ax[1].set_axes_locator(divider.new_locator(nx=2, ny=0)) ax[2].set_axes_locator(divider.new_locator(nx=0, ny=2)) ax[3].set_axes_locator(divider.new_locator(nx=2, ny=2)) ax[0].set_xlim(0, 2) ax[1].set_xlim(0, 1) ax[0].set_ylim(0, 1) ax[2].set_ylim(0, 2) divider.set_aspect(1.)
os.remove(temppath)
size(W, HEIGHT+dy+40)
else:
def pltshow(mplpyplot):
mplpyplot.show()
# nodebox section end
fig1 = plt.figure(1, (6, 6))
# fixed size in inch
horiz = [Size.Fixed(1.), Size.Fixed(.5), Size.Fixed(1.5),
Size.Fixed(.5)]
vert = [Size.Fixed(1.5), Size.Fixed(.5), Size.Fixed(1.)]
rect = (0.1, 0.1, 0.8, 0.8)
# divide the axes rectangle into grid whose size is specified by horiz * vert
divider = Divider(fig1, rect, horiz, vert, aspect=False)
# the rect parameter will be ignore as we will set axes_locator
ax1 = fig1.add_axes(rect, label="1")
ax2 = fig1.add_axes(rect, label="2")
ax3 = fig1.add_axes(rect, label="3")
ax4 = fig1.add_axes(rect, label="4")
ax1.set_axes_locator(divider.new_locator(nx=0, ny=0))
ax2.set_axes_locator(divider.new_locator(nx=0, ny=2))
ax3.set_axes_locator(divider.new_locator(nx=2, ny=2))
ax4.set_axes_locator(divider.new_locator(nx=2, nx1=4, ny=0))
pltshow(plt)
def _setup_image_grid(self, figure, dims):
"""
An example of how grid, parameter and view numbers change
for dims = 4
The numbers in the grid are:
parameter x, parameter y
grid x, grid y
-----------------------------------------------------
| | | | |
| 0, 0 | 1, 0 | 2, 0 | 3, 0 |
| -, - | -, - | -, - | -, - |
| | | | |
==============------------|------------|------------|
I I | | |
I 0, 1 I 1, 1 | 2, 1 | 3, 1 |
I 0, 0 I 1, 0 | 2, 0 | -, - |
I I | | |
I------------==============------------|------------|
I | I | |
I 0, 2 | 1, 2 I 2, 2 | 3, 2 |
I 0, 1 | 1, 1 I 2, 1 | -, - |
I | I | |
I------------|------------==============------------|
I | | I |
I 0, 3 | 1, 3 | 2, 3 I 3, 3 |
I 0, 2 | 1, 2 | 2, 2 I -, - |
I | | I |
I======================================I------------|
From the above it should be clear that:
parameter x = grid x
parameter y = grid y + 1
grid nr = grid y + grid x * (dims - 1)
view nr = grid nr - (grid nr / dims) * ((grid nr / dims) +1) / 2
"""
image_grid = ImageGrid(
figure,
111,
nrows_ncols=(dims - 1, dims - 1),
cbar_location="right",
cbar_mode="single",
# add_all=False,
aspect=False,
axes_pad=0.1,
direction="column")
rect = (0.1, 0.1, 0.8, 0.8)
horiz = [Size.Fixed(.1)
] + [Size.Scaled(1.), Size.Fixed(.1)] * max(dims - 1, 1) + [
Size.Fixed(0.15)
]
vert = [Size.Fixed(.1)
] + [Size.Scaled(1.), Size.Fixed(.1)] * max(dims - 1, 1)
# divide the axes rectangle into grid whose size is specified by horiz * vert
divider = Divider(figure, rect, horiz, vert) # , aspect=False)
# Helper to get the axis for par x and y:
def get_grid(parx, pary):
gridx = parx
gridy = pary - 1
return image_grid[gridy + gridx * (dims - 1)]
# Helper to get the grid locator for par x and par y
def get_locator(parx, pary):
gridx = parx
gridy = pary - 1
nx = 1 + gridx * 2
ny = 1 + (dims - gridy - 2) * 2
return divider.new_locator(nx=nx, ny=ny)
# Hide the unused plots & setup the used ones:
for parx, pary in itertools.product(list(range(self.num_params - 1)),
list(range(1, self.num_params))):
# Calculate the grid position:
ax = get_grid(parx, pary)
# Setup axes:
if pary <= parx:
ax.set_visible(False)
else:
ax.set_axes_locator(get_locator(parx, pary))
ax.set_visible(True)
return image_grid, divider, get_grid
=====================
"""
import mpl_toolkits.axes_grid1.axes_size as Size
from mpl_toolkits.axes_grid1 import Divider
import matplotlib.pyplot as plt
fig1 = plt.figure(1, (5.5, 4.))
# the rect parameter will be ignore as we will set axes_locator
rect = (0.1, 0.1, 0.8, 0.8)
ax = [fig1.add_axes(rect, label="%d" % i) for i in range(4)]
horiz = [Size.Scaled(1.5), Size.Fixed(.5), Size.Scaled(1.), Size.Scaled(.5)]
vert = [Size.Scaled(1.), Size.Fixed(.5), Size.Scaled(1.5)]
# divide the axes rectangle into grid whose size is specified by horiz * vert
divider = Divider(fig1, rect, horiz, vert, aspect=False)
ax[0].set_axes_locator(divider.new_locator(nx=0, ny=0))
ax[1].set_axes_locator(divider.new_locator(nx=0, ny=2))
ax[2].set_axes_locator(divider.new_locator(nx=2, ny=2))
ax[3].set_axes_locator(divider.new_locator(nx=2, nx1=4, ny=0))
for ax1 in ax:
plt.setp(ax1.get_xticklabels() + ax1.get_yticklabels(), visible=False)
plt.draw()
plt.show()
labelleft=False)
##############################################################################
# Fixed axes sizes; fixed paddings.
fig = plt.figure(figsize=(6, 6))
fig.suptitle("Fixed axes sizes, fixed paddings")
# Sizes are in inches.
horiz = [Size.Fixed(1.), Size.Fixed(.5), Size.Fixed(1.5), Size.Fixed(.5)]
vert = [Size.Fixed(1.5), Size.Fixed(.5), Size.Fixed(1.)]
rect = (0.1, 0.1, 0.8, 0.8)
# Divide the axes rectangle into a grid with sizes specified by horiz * vert.
div = Divider(fig, rect, horiz, vert, aspect=False)
# The rect parameter will actually be ignored and overridden by axes_locator.
ax1 = fig.add_axes(rect, axes_locator=div.new_locator(nx=0, ny=0))
label_axes(ax1, "nx=0, ny=0")
ax2 = fig.add_axes(rect, axes_locator=div.new_locator(nx=0, ny=2))
label_axes(ax2, "nx=0, ny=2")
ax3 = fig.add_axes(rect, axes_locator=div.new_locator(nx=2, ny=2))
label_axes(ax3, "nx=2, ny=2")
ax4 = fig.add_axes(rect, axes_locator=div.new_locator(nx=2, nx1=4, ny=0))
label_axes(ax4, "nx=2, nx1=4, ny=0")
##############################################################################
# Axes sizes that scale with the figure size; fixed paddings.
fig = plt.figure(figsize=(6, 6))
def setup_axes(df, plates, attrs):
from mpl_toolkits.axes_grid1 import Divider
from mpl_toolkits.axes_grid1.axes_size import Fixed
# These assumptions let us simplify some code, and should always be true.
assert len(plates) > 0
assert len(attrs) > 0
# Determine how much data will be shown in the figure:
num_plates = len(plates)
num_attrs = len(attrs)
dims = Dimensions(df)
bar_label_width = guess_attr_label_width(df, attrs)
# Define the grid on which the axes will live:
h_divs = [
LEFT_MARGIN,
]
for _ in plates:
h_divs += [
CELL_SIZE * dims.num_cols,
PAD_WIDTH,
]
h_divs[-1:] = [
BAR_PAD_WIDTH,
BAR_WIDTH,
RIGHT_MARGIN + bar_label_width,
]
v_divs = [
TOP_MARGIN,
]
for attr in attrs:
v_divs += [
max(
CELL_SIZE * dims.num_rows,
BAR_WIDTH * dims.num_values[attr],
),
PAD_HEIGHT,
]
v_divs[-1:] = [
BOTTOM_MARGIN,
]
# Add up all the divisions to get the width and height of the figure:
figsize = sum(h_divs), sum(v_divs)
# Make the figure:
fig, axes = plt.subplots(
num_attrs,
num_plates + 1, # +1 for the colorbar axes.
figsize=figsize,
squeeze=False,
)
# Position the axes:
rect = 0.0, 0.0, 1, 1
h_divs = [Fixed(x) for x in h_divs]
v_divs = [Fixed(x) for x in reversed(v_divs)]
divider = Divider(fig, rect, h_divs, v_divs, aspect=False)
for i in range(num_attrs):
for j in range(num_plates + 1):
loc = divider.new_locator(nx=2 * j + 1, ny=2 * (num_attrs - i) - 1)
axes[i, j].set_axes_locator(loc)
return fig, axes, dims
def cpu_svg(self,
host=None,
title="CPU Usage",
ylabel="Percent",
b64encode=True):
fig = pyplot.figure(figsize=self.FIGSIZE)
h = [Size.Fixed(1.2), Size.Scaled(1.), Size.Fixed(.2)]
v = [Size.Fixed(0.7), Size.Scaled(1.), Size.Fixed(.5)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
plt = Axes(fig, divider.get_position())
plt.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(plt)
result = self.result
runinfo = result.runinfo
# ----
# The X limits are -rampupMins, runMins, Y limits are 0..100
# ----
plt.set_xlim(-int(runinfo['rampupMins']), int(runinfo['runMins']))
plt.set_ylim(0, 100)
plt.axvspan(-int(runinfo['rampupMins']), 0, facecolor='0.2', alpha=0.1)
# ----
# Gather all the relevant data
# ----
x, y_user = self._get_metric_xy({
'host': host,
'metric': 'cpu.percent-user',
})
_, y_sys = self._get_metric_xy(
{
'host': host,
'metric': 'cpu.percent-system',
}, x)
_, y_wait = self._get_metric_xy(
{
'host': host,
'metric': 'cpu.percent-wait',
}, x)
_, y_intr = self._get_metric_xy(
{
'host': host,
'metric': 'cpu.percent-interrupt',
}, x)
_, y_softirq = self._get_metric_xy(
{
'host': host,
'metric': 'cpu.percent-softirq',
}, x)
_, y_idle = self._get_metric_xy(
{
'host': host,
'metric': 'cpu.percent-idle',
}, x)
# ----
# It is possible that the mqtt based metric collector produces
# CSV files with different numbers of lines. We cut all of them
# to a combined minimum length.
# ----
min_len = min(len(x), len(y_user), len(y_sys), len(y_wait),
len(y_intr), len(y_softirq), len(y_idle))
x = x[:min_len]
y_user = y_user[:min_len]
y_sys = y_sys[:min_len]
y_wait = y_wait[:min_len]
y_intr = y_intr[:min_len]
y_softirq = y_softirq[:min_len]
y_idle = y_idle[:min_len]
# ----
# Plot the CPU usage
# ----
plt.stackplot(x,
y_user,
y_sys,
y_wait,
y_intr,
y_softirq,
y_idle,
colors=[
'g',
'b',
'r',
'c',
'm',
'y',
],
labels=[
'User',
'System',
'Wait',
'Interrupt',
'SoftIrq',
'Idle',
])
# ----
# Title and labels
# ----
plt.set_title(title)
plt.set_xlabel("Elapsed Minutes")
plt.set_ylabel(ylabel)
plt.legend(loc='upper left')
plt.grid()
# ----
# Now turn this into an in-memory SVG and return it as requested
# (raw or b64-encoded)
# ----
buf = io.StringIO()
pyplot.savefig(buf, format='svg')
if not b64encode:
return buf.getvalue()
return base64.b64encode(buf.getvalue().encode('utf-8')).decode('utf-8')
def tpmc_svg(self, b64encode=True):
fig = pyplot.figure(figsize=self.FIGSIZE)
h = [Size.Fixed(1.2), Size.Scaled(1.), Size.Fixed(.2)]
v = [Size.Fixed(0.7), Size.Scaled(1.), Size.Fixed(.5)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
plt = Axes(fig, divider.get_position())
plt.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(plt)
result = self.result
runinfo = result.runinfo
# ----
# The X limits are -rampupMins, runMins
# ----
plt.set_xlim(-int(runinfo['rampupMins']), int(runinfo['runMins']))
plt.axvspan(-int(runinfo['rampupMins']), 0, facecolor='0.2', alpha=0.1)
# ----
# offset the timestamps by -rampupMins so that the graph
# starts with negative minutes elapsed and switches to
# positive when the measurement begins.
# ----
offset = (int(runinfo['rampupMins'])) * 60.0
# ----
# NEW_ORDER transactions per minute. First get the timestamp
# and number of transactions from the result data.
# The X vector then is the sorted unique timestamps rounded
# to an interval.
# ----
interval = 10
data = numpy.array([[(int(tup[0] / interval) * interval - offset) / 60,
tup[1] * (60 / interval)]
for tup in result.result_ttype['NEW_ORDER']])
x = sorted(numpy.unique(data[:, 0]))
# ----
# The Y vector is the sums of transactions grouped by X
# ----
y = []
for ts in x:
tmp = data[numpy.where(data[:, 0] == ts)]
y.append(numpy.sum(tmp[:, 1]))
# ----
# Plot the NOPM and add all the decorations
# ----
plt.plot(x, y, 'b')
plt.set_title("NEW_ORDER Transactions per Minute (tpmC)")
plt.set_xlabel("Elapsed Minutes")
plt.set_ylabel("tpmC")
plt.grid()
buf = io.StringIO()
pyplot.savefig(buf, format='svg')
if not b64encode:
return buf.getvalue()
return base64.b64encode(buf.getvalue().encode('utf-8')).decode('utf-8')
sumFinalAnalysis = sum(lstFinalAnalysis)
sumFinalAnalysisTE = np.matmul(-np.transpose(npTE), lstFinalAnalysis)
A = np.array([[ndados, sumTE], [sumTE, prodTE]])
B = np.array([[sumFinalAnalysis], [sumFinalAnalysisTE]])
invA = np.linalg.inv(A)
P = np.matmul(invA, B)
T2[indexValue] = (P[1][0])
for i, t in enumerate(T2):
T2[i] = math.inf if t[0] == 0 else 1000 / t[0]
T2Star = np.reshape(T2, (400, 400))
fig = plt.figure(figsize=(6, 6))
h = [Size.Fixed(1.0), Size.Fixed(5.)]
v = [Size.Fixed(1.0), Size.Fixed(5.)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
ax = Axes(fig, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(ax)
plt.pcolor(np.flip(T2Star, 0), cmap=jet_combined, vmin=0, vmax=180)
toc = time.perf_counter()
print(f"Executed in {toc - tic:0.4f} seconds")
# toggle_selector.RS = RectangleSelector(ax, line_select_callback,
# drawtype='box', useblit=True,
# button=[1, 3], # don't use middle button
# minspanx=5, minspany=5,
# spancoords='pixels',
# interactive=True)
# plt.connect('key_press_event', toggle_selector)
def memory_svg(self,
host=None,
title="Memory Usage",
unit="Bytes",
factor=1.0,
b64encode=True):
fig = pyplot.figure(figsize=self.FIGSIZE)
h = [Size.Fixed(1.2), Size.Scaled(1.), Size.Fixed(.2)]
v = [Size.Fixed(0.7), Size.Scaled(1.), Size.Fixed(.5)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
plt = Axes(fig, divider.get_position())
plt.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(plt)
result = self.result
runinfo = result.runinfo
# ----
# The X limits are -rampupMins, runMins
# ----
plt.set_xlim(-int(runinfo['rampupMins']), int(runinfo['runMins']))
plt.axvspan(-int(runinfo['rampupMins']), 0, facecolor='0.2', alpha=0.1)
x, y_used = self._get_metric_xy({
'host': host,
'metric': 'memory.memory-used',
'factor': factor,
})
_, y_cached = self._get_metric_xy(
{
'host': host,
'metric': 'memory.memory-cached',
'factor': factor,
}, x)
_, y_buffered = self._get_metric_xy(
{
'host': host,
'metric': 'memory.memory-buffered',
'factor': factor,
}, x)
_, y_free = self._get_metric_xy(
{
'host': host,
'metric': 'memory.memory-free',
'factor': factor,
}, x)
# ----
# It is possible that the mqtt based metric collector produces
# CSV files with different numbers of lines. We cut all of them
# to a combined minimum length.
# ----
min_len = min(len(x), len(y_used), len(y_cached), len(y_buffered),
len(y_free))
x = x[:min_len]
y_used = y_used[:min_len]
y_cached = y_cached[:min_len]
y_buffered = y_buffered[:min_len]
y_free = y_free[:min_len]
plt.stackplot(x,
y_used,
y_cached,
y_buffered,
y_free,
colors=[
'b',
'y',
'g',
'gray',
],
labels=[
'Used',
'Cached',
'Buffered',
'Free',
])
# ----
# Title and labels
# ----
plt.set_title(title)
plt.set_xlabel("Elapsed Minutes")
plt.set_ylabel(unit)
plt.legend(loc='upper left')
plt.grid()
# ----
# Now turn this into an in-memory SVG and return it as requested
# (raw or b64-encoded)
# ----
buf = io.StringIO()
pyplot.savefig(buf, format='svg')
if not b64encode:
return buf.getvalue()
return base64.b64encode(buf.getvalue().encode('utf-8')).decode('utf-8')
def plot_variance_multi(savefile,
data,
labels,
colors,
ylabel,
ylim,
ylim_unit=1,
ylim_scale=5,
colors2=None,
hline=None,
vline=None,
locator=-1,
draw_dist=True,
subsample=1):
plt.clf()
plt.rcParams["font.size"] = 14
colors2 = colors if colors2 is None else colors2
m = len(data)
#fig, ax = plt.subplots(1, 1)
fig = plt.figure(1, figsize=(4, 4))
# The first items are for padding and the second items are for the axes.
# sizes are in inch.
h = [Size.Fixed(0.65), Size.Fixed(5.5)]
v = [Size.Fixed(0.7), Size.Fixed(4.)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
# the width and height of the rectangle is ignored.
ax = LocatableAxes(fig, divider.get_position())
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(ax)
if not hasattr(draw_dist, '__getitem__'):
v = draw_dist
draw_dist = [v for i in range(m)]
print(draw_dist)
for k in range(m)[::-1]:
plot_m = numpy.median(data[k], 0)
sorted = numpy.sort(data[k], 0)
n = data[k].shape[0]
T = data[k].shape[1]
t = numpy.arange(0, T)
fin = plot_m[-1]
best = sorted[0][-1]
alpha = 1.0 / (n // 2) * 0.4
if subsample > 1:
t = subsample_data(t, subsample)
plot_m = subsample_data(plot_m, subsample)
sorted = subsample_data(sorted, subsample)
if k == 0:
if ylim is None:
ymax = min([fin * ylim_scale, sorted[-1, 0], 90])
ymin = numpy.floor(numpy.max(best / ylim_unit - 0.5,
0)) * ylim_unit
ymin = 0
ylim = [ymin, numpy.ceil(ymax / ylim_unit) * ylim_unit]
else:
ylim = ylim
# 3: 0
if draw_dist[k]:
print('k', k)
for i in range(n // 2):
ax.fill_between(t,
sorted[-1 - i],
sorted[i],
facecolor=colors2[k],
alpha=alpha)
for k in range(m)[::-1]:
plot_m = numpy.median(data[k], 0)
t = numpy.arange(0, T)
if subsample > 1:
t = subsample_data(t, subsample)
plot_m = subsample_data(plot_m, subsample)
ax.plot(t, plot_m, lw=1, color=colors[k], ls='-', label=labels[k])
if hline is not None:
ax.plot((0, T), (hline, hline), color='gray', ls=':')
if vline is not None:
ax.plot((vline, vline), (ylim[0], ylim[1]), color='gray', ls=':')
ax.legend(loc='upper right')
ax.set_xlabel('Iterations')
ax.set_ylabel(ylabel)
ax.set_xlim([0, T])
ax.set_ylim(ylim)
if locator >= 0:
ax.yaxis.set_major_locator(MultipleLocator(locator))
ax.grid()
plt.savefig(savefile + '.png')
plt.savefig(savefile + '.pdf')
import mpl_toolkits.axes_grid1.axes_size as Size
from mpl_toolkits.axes_grid1 import Divider
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(5.5, 4))
rect = (0.1, 0.1, 0.8, 0.8)
ax = [fig.add_axes(rect, label="%d" % i) for i in range(4)]
horiz = [Size.AxesX(ax[0]), Size.Fixed(.5), Size.AxesX(ax[1])]
vert = [Size.AxesY(ax[0]), Size.Fixed(.5), Size.AxesY(ax[2])]
divider = Divider(fig, rect, horiz, vert, aspect=False)
ax[0].set_axes_locator(divider.new_locator(nx=0, ny=0))
ax[1].set_axes_locator(divider.new_locator(nx=2, ny=0))
ax[2].set_axes_locator(divider.new_locator(nx=0, ny=2))
ax[3].set_axes_locator(divider.new_locator(nx=2, ny=2))
ax[0].set_xlim(0, 2)
ax[1].set_xlim(0, 1)
ax[0].set_ylim(0, 1)
ax[2].set_ylim(0, 2)
divider.set_aspect(1.)
for ax1 in ax:
ax1.tick_params(labelbottom=False, labelleft=False)
plt.show()
def plot_legend(self, legend_unit_height=0.25):
"""
Plot a legend for this Style object.
If the color and width labels are the same, a single legend will
be created. Otherwise, two legends will be created - one with
the color labels, and the other with the width labels.
Parameters
----------
legend_unit_height : float
A scaling factor to modify the height of each unit in the
legend only.
Returns
-------
fig : matplotlib Figure
Figure handle.
ax : matplotlib Axes
Axis handle.
"""
# print some plotting values
print('stratigraphic height scaling : 1 distance unit = 1 inch * {}'.
format(self.height_scaling_factor))
print('width value of 1 will be : {} inches'.format(
self.width_inches))
# extract attributes
color_labels = self.color_labels
width_labels = self.width_labels
color_values = self.color_values
width_values = self.width_values
# if the color and width labels are different
if np.any(~(color_labels == width_labels)):
# sort the widths
width_sort_inds = np.argsort(width_values)
width_labels = width_labels[width_sort_inds]
width_values = width_values[width_sort_inds]
# initialize the figure
fig, ax = plt.subplots(nrows=1, ncols=2, sharey=True)
# determine the axis height and limits first
if self.n_color_labels > self.n_width_labels:
ax_height = legend_unit_height * self.n_color_labels
ax[0].set_ylim(0, self.n_color_labels)
ax[1].set_ylim(0, self.n_color_labels)
else:
ax_height = legend_unit_height * self.n_width_labels
ax[0].set_ylim(0, self.n_width_labels)
ax[1].set_ylim(0, self.n_width_labels)
# plot the colors
strat_height_colors = 0
for i in range(len(color_labels)):
# create the rectangle - with thickness of 1
ax[0].add_patch(
Rectangle((0.0, strat_height_colors),
1,
1,
facecolor=color_values[i],
edgecolor='k'))
# label the unit
ax[0].text(1.2,
strat_height_colors + 0.5,
color_labels[i],
horizontalalignment='left',
verticalalignment='center')
# count the height
strat_height_colors = strat_height_colors + 1
# set the axis dimensions (values below are all in inches)
ax0_lower_left_x = 0.5
ax0_lower_left_y = 0.5
ax0_width = 0.5
h = [Size.Fixed(ax0_lower_left_x), Size.Fixed(ax0_width)]
v = [Size.Fixed(ax0_lower_left_y), Size.Fixed(ax_height)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
ax[0].set_axes_locator(divider.new_locator(nx=1, ny=1))
# set the limits
ax[0].set_xlim(0, 1)
# prettify
ax[0].set_xticks([])
ax[0].set_yticklabels([])
ax[0].set_yticks([])
# plot the widths
strat_height_widths = 0
for i in range(len(width_labels)):
# create the rectangle
ax[1].add_patch(
Rectangle((0.0, strat_height_widths),
width_values[i],
1,
facecolor='grey',
edgecolor='k'))
# the label
ax[1].text(1.1,
strat_height_widths + 0.5,
width_labels[i],
horizontalalignment='left',
verticalalignment='center')
# count the height
strat_height_widths = strat_height_widths + 1
# set the axis dimensions (values below are all in inches)
ax1_lower_left_x = ax0_lower_left_x + ax0_width + 2
ax1_lower_left_y = ax0_lower_left_y
ax1_width = self.width_inches
h = [Size.Fixed(ax1_lower_left_x), Size.Fixed(ax1_width)]
v = [Size.Fixed(ax1_lower_left_y), Size.Fixed(ax_height)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
ax[1].set_axes_locator(divider.new_locator(nx=1, ny=1))
# prettify
ax[1].set_xlim(0, 1)
ax[1].set_xticks([0, 0.2, 0.4, 0.6, 0.8, 1])
for label in ax[1].get_xticklabels():
label.set_rotation(270)
label.set_ha('center')
label.set_va('top')
ax[1].set_axisbelow(True)
ax[1].xaxis.grid(ls='--')
ax[1].set_yticklabels([])
ax[1].set_yticks([])
ax[1].spines['top'].set_visible(False)
ax[1].spines['right'].set_visible(False)
# turning the spines off creates some clipping mask issues
# so just turn the clipping masks off
for obj in fig.findobj():
obj.set_clip_on(False)
# not really necessary since the axis sizes are already
# forced, but we may as well set the figsize here too
fig.set_size_inches(
ax1_lower_left_x + ax1_width + ax0_lower_left_x,
ax1_lower_left_y * 2 + ax_height)
# if the color and width labels are the same
else:
# sort by width
width_sort_inds = np.argsort(width_values)
color_labels = color_labels[width_sort_inds]
width_labels = width_labels[width_sort_inds]
color_values = color_values[width_sort_inds]
width_values = width_values[width_sort_inds]
# initiate fig and ax
fig, ax = plt.subplots()
# determine the axis height and limits first
ax_height = legend_unit_height * self.n_color_labels
ax.set_ylim(0, self.n_color_labels)
# initiate counting of the stratigraphic height
strat_height = 0
# loop over each item
for i in range(len(color_labels)):
# create the rectangle - with thickness of 1
ax.add_patch(
Rectangle((0.0, strat_height),
width_values[i],
1,
facecolor=color_values[i],
edgecolor='k'))
# label the unit
ax.text(1.1,
strat_height + 0.5,
color_labels[i],
horizontalalignment='left',
verticalalignment='center')
# count the stratigraphic height
strat_height = strat_height + 1
# set the axis dimensions (values below are all in inches)
ax_lower_left_x = 0.5
ax_lower_left_y = 0.5
ax_width = self.width_inches
h = [Size.Fixed(ax_lower_left_x), Size.Fixed(ax_width)]
v = [Size.Fixed(ax_lower_left_y), Size.Fixed(ax_height)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
ax.set_axes_locator(divider.new_locator(nx=1, ny=1))
# prettify
ax.set_xlim(0, 1)
ax.set_xticks([0, 0.2, 0.4, 0.6, 0.8, 1])
for label in ax.get_xticklabels():
label.set_rotation(270)
label.set_ha('center')
label.set_va('top')
ax.set_axisbelow(True)
ax.xaxis.grid(ls='--')
ax.set_yticklabels([])
ax.set_yticks([])
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
# turning the spines off creates some clipping mask issues
# so just turn the clipping masks off
for obj in fig.findobj():
obj.set_clip_on(False)
# not really necessary since the axis sizes are already
# forced, but we may as well set the figsize here too
fig.set_size_inches(ax_lower_left_x * 2 + ax_width,
ax_lower_left_y * 2 + ax_height)
return fig, ax
ax3 = divider.append_axes('right', size='33%', pad=0.5)
ax3.plot(t, x3)
# <markdowncell>
# make_axes_locatable() gives one way to handle this, by giving the append_axes() method. Another way is by creating a Divider object and giving it the layout up front.
# <codecell>
from mpl_toolkits.axes_grid1 import Size, Divider
fig = plt.figure()
ax = [fig.add_axes([0.1,0.1,0.8,0.8], label='%d'%i) for i in range(3)] # Create 3 Axes to be sized later
horiz = [Size.Scaled(2), Size.Fixed(0.5), Size.Scaled(3), Size.Fixed(0.01)]
vert = [Size.Scaled(1), Size.Fixed(0.5), Size.Scaled(1)]
div = Divider(fig, (0.1, 0.1, 0.8, 0.8), horiz, vert, aspect=False)
ax[0].set_axes_locator(div.new_locator(nx=0, ny=0))
ax[1].set_axes_locator(div.new_locator(nx=2, ny=0))
ax[2].set_axes_locator(div.new_locator(nx=0, nx1=2, ny=2))
ax[0].plot(t, x1)
ax[1].plot(t, x2)
ax[2].plot(t, x3)
# <rawcell>
# One obvious application of this is for doing grid of plots with colorbars. For this use case we can go one step further and make use of the ImageGrid class.
# <codecell>
def plot_stratigraphy(section,
style,
ncols=1,
linewidth=1,
col_spacings=0.5,
col_widths=1):
"""
Initialize a figure and subplots, with the stratigraphic section
already plotted on the first axis.
This function is intended to act similar to `plt.subplots()` in that
it will initialize the figure and axis handles. However, given that
controlling the exact width and height of the axes is critical, this
function is necessary to initialize the handles correctly.
Note that setting the figsize itself is not sufficient to control
the width and height of the axes exactly, since the figsize includes
the size of the padding around the axes.
Parameters
----------
section : Section
A Section object.
style : Style
A Style object.
ncols : int
The number of axes that will be in the figure (including the
axis with the stratigraphic section.)
linewidth : float
The linewidth when drawing the stratigraphic section.
col_spacings : float or array_like
The spacing between the axes in inches. If a float, this value
will be interpreted as uniform spacing between the axes. If an
array, the length of the array must be ncols - 1, and the values
will be the spacing between the individual axes.
col_widths : float or array_like
The width of the axes as a ratio relative to the width of the
stratigraphic column. If a float, this value will be interpreted
as a uniform width of the axes, excluding the stratigraphic
column, for which the width is explicitly set in the Style. If
an array, the length of the array must be ncols - 1, and the
values will be the widths of the individual axes excluding the
stratigraphic column.
Returns
-------
fig : matplotlib Figure
Figure handle.
ax : matplotlib Axes
Axis handle.
"""
# get the attributes - implicitly checks if the attributes exist
color_attribute = getattr(section, style.color_attribute)
width_attribute = getattr(section, style.width_attribute)
# initialize
fig, ax = plt.subplots(nrows=1, ncols=ncols, sharey=True)
# get the first axis
if ncols == 1:
ax0 = ax
else:
ax0 = ax[0]
# determine the axis height and limits first
ax_height = style.height_scaling_factor * section.total_thickness
ax0.set_ylim(0, section.total_thickness)
# initiate counting of the stratigraphic height
strat_height = 0.0
# loop over elements of the data
for i in range(section.n_units):
# pull out the thickness
this_thickness = section.thicknesses[i]
# loop over the elements in Style to get the color and width
for j in range(style.n_color_labels):
if color_attribute[i] == style.color_labels[j]:
this_color = style.color_values[j]
for j in range(style.n_width_labels):
if width_attribute[i] == style.width_labels[j]:
this_width = style.width_values[j]
# create the rectangle
ax0.add_patch(
Rectangle((0.0, strat_height),
this_width,
this_thickness,
facecolor=this_color,
edgecolor='k',
linewidth=linewidth))
# count the stratigraphic height
strat_height = strat_height + this_thickness
# set the axis dimensions (values below are all in inches)
ax0_lower_left_x = 0.5
ax0_lower_left_y = 0.5
ax0_width = style.width_inches
h = [Size.Fixed(ax0_lower_left_x), Size.Fixed(ax0_width)]
v = [Size.Fixed(ax0_lower_left_y), Size.Fixed(ax_height)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
ax0.set_axes_locator(divider.new_locator(nx=1, ny=1))
# prettify
ax0.set_xlim(0, 1)
ax0.set_xticks([0, 0.2, 0.4, 0.6, 0.8, 1])
for label in ax0.get_xticklabels():
label.set_rotation(270)
label.set_ha('center')
label.set_va('top')
ax0.set_axisbelow(True)
ax0.xaxis.grid(ls='--')
ax0.spines['top'].set_visible(False)
ax0.spines['right'].set_visible(False)
ax0.set_ylabel('stratigraphic height [m]')
# turning the spines off creates some clipping mask issues
# so just turn the clipping masks off
for obj in ax0.findobj():
obj.set_clip_on(False)
# check if the col_spacing and col_widths is of the correct format
if type(col_spacings) == list or type(col_spacings) == np.ndarray:
if len(col_spacings) != ncols - 1:
raise Exception('col_spacings must be either a float or '
'array_like with length ncols-1.')
if type(col_widths) == list or type(col_widths) == np.ndarray:
if len(col_widths) != ncols - 1:
raise Exception('col_widths must be either a float or '
'array_like with length ncols-1.')
# set up the other axes
if ncols != 1:
# iterate through the axes
for i in range(1, ncols):
# get the spacing and width values
if type(col_spacings) == list or type(col_spacings) == np.ndarray:
col_spacing = col_spacings[i - 1]
else:
col_spacing = col_spacings
if type(col_widths) == list or type(col_widths) == np.ndarray:
col_width = col_widths[i - 1] * ax0_width
else:
col_width = col_widths * ax0_width
# adjust the axis
if i == 1:
axn_lower_left_x = ax0_lower_left_x + ax0_width + col_spacing
else:
axn_lower_left_x = axn_lower_left_x + axn_width + col_spacing
axn_lower_left_y = ax0_lower_left_y
axn_width = col_width
h = [Size.Fixed(axn_lower_left_x), Size.Fixed(axn_width)]
v = [Size.Fixed(axn_lower_left_y), Size.Fixed(ax_height)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
ax[i].set_axes_locator(divider.new_locator(nx=1, ny=1))
# set the figsize here too to account for the axis size manipulation
if ncols != 1:
fig.set_size_inches(
ax0_lower_left_x * 2 + np.sum(col_spacings) + np.sum(col_widths) +
ax0_width, ax0_lower_left_y * 2 + ax_height)
else:
fig.set_size_inches(ax0_lower_left_x * 2 + ax0_width,
ax0_lower_left_y * 2 + ax_height)
return fig, ax
class MatPlotLibBase(QWidget):
def __init__(self,
parent,
file_dialog_service,
h_margin=(0.8, 0.1),
v_margin=(0.5, 0.15),
h_axes=[Size.Scaled(1.0)],
v_axes=[Size.Scaled(1.0)],
nx_default=1,
ny_default=1):
QWidget.__init__(self, parent)
self._file_dialog_service = file_dialog_service
self._figure = Figure()
self._canvas = FigureCanvas(self._figure)
h = [Size.Fixed(h_margin[0]), *h_axes, Size.Fixed(h_margin[1])]
v = [Size.Fixed(v_margin[0]), *v_axes, Size.Fixed(v_margin[1])]
self._divider = Divider(self._figure, (0.0, 0.0, 1.0, 1.0),
h,
v,
aspect=False)
self._axes = LocatableAxes(self._figure, self._divider.get_position())
self._axes.set_axes_locator(
self._divider.new_locator(nx=nx_default, ny=ny_default))
self._axes.set_zorder(2)
self._axes.patch.set_visible(False)
for spine in ['top', 'right']:
self._axes.spines[spine].set_visible(False)
self._figure.add_axes(self._axes)
self._canvas.setParent(self)
self._layout = QVBoxLayout(self)
self._layout.setContentsMargins(0, 0, 0, 0)
self._layout.addWidget(self._canvas)
self.setLayout(self._layout)
self._figure.canvas.mpl_connect('scroll_event', self._on_scroll)
self._xy_extents = None
self._background_cache = None
self._decoration_artists = []
self._is_panning = False
self._zoom_selector = _RectangleSelector(self._axes,
self._zoom_selected)
self._zoom_selector.set_active(False)
self._x_extent_padding = 0.01
self._y_extent_padding = 0.01
self._axes.ticklabel_format(style='sci', axis='x', scilimits=(-4, 4))
self._axes.ticklabel_format(style='sci', axis='y', scilimits=(-4, 4))
self._active_tools = {}
self._span = _SpanSeletor(self._axes,
self._handle_span_select,
'horizontal',
rectprops=dict(alpha=0.2,
facecolor='red',
edgecolor='k'),
span_stays=True)
self._span.set_on_select_none(self._handle_span_select_none)
self.span = self._previous_span = None
self._span_center_mouse_event = None
self._span_left_mouse_event = None
self._span_right_mouse_event = None
self._figure.canvas.mpl_connect('button_press_event',
self._handle_press)
self._figure.canvas.mpl_connect('motion_notify_event',
self._handle_move)
self._figure.canvas.mpl_connect('button_release_event',
self._handle_release)
self._figure.canvas.mpl_connect('resize_event', self._handle_resize)
self.activateTool(ToolType.span, self.isActiveDefault(ToolType.span))
self._pan_event = None
self._pending_draw = None
self._pending_artists_draw = None
self._other_draw_events = []
self._draw_timer = QTimer(self)
self._draw_timer.timeout.connect(self._do_draw_events)
self._draw_timer.start(20)
self._zoom_skew = None
self._menu = QMenu(self)
self._copy_image_action = QAction(self.tr('Copy To Clipboard'), self)
self._copy_image_action.triggered.connect(self.copyToClipboard)
self._copy_image_action.setShortcuts(QKeySequence.Copy)
self._save_image_action = QAction(self.tr('Save As Image'), self)
self._save_image_action.triggered.connect(self.saveAsImage)
self._show_table_action = QAction(self.tr('Show Table'), self)
self._show_table_action.triggered.connect(self.showTable)
self._menu.addAction(self._copy_image_action)
self._menu.addAction(self._save_image_action)
self._menu.addAction(self._show_table_action)
self.addAction(self._copy_image_action)
self._table_view = None
self._single_axis_zoom_enabled = True
self._cached_label_width_height = None
if hasattr(type(self), 'dataChanged'):
self.dataChanged.connect(self._on_data_changed)
self._options_view = None
self._secondary_axes = self._secondary_y_extent = self._secondary_x_extent = None
self._legend = None
self._draggable_legend = None
self._setting_axis_limits = False
self.hasHiddenSeries = False
enabledToolsChanged = pyqtSignal()
spanChanged = pyqtSignal(SpanModel)
hasHiddenSeriesChanged = pyqtSignal(bool)
span = AutoProperty(SpanModel)
hasHiddenSeries = AutoProperty(bool)
def setOptionsView(self, options_view):
self._options_view = options_view
self._options_view.setSecondaryYLimitsEnabled(
self._secondary_y_enabled())
self._options_view.setSecondaryXLimitsEnabled(
self._secondary_x_enabled())
self._options_view.showGridLinesChanged.connect(
self._update_grid_lines)
self._options_view.xAxisLowerLimitChanged.connect(
self._handle_options_view_limit_changed(x_min_changed=True))
self._options_view.xAxisUpperLimitChanged.connect(
self._handle_options_view_limit_changed(x_max_changed=True))
self._options_view.yAxisLowerLimitChanged.connect(
self._handle_options_view_limit_changed(y_min_changed=True))
self._options_view.yAxisUpperLimitChanged.connect(
self._handle_options_view_limit_changed(y_max_changed=True))
self._options_view.xAxisLimitsChanged.connect(
self._handle_options_view_limit_changed(x_min_changed=True,
x_max_changed=True))
self._options_view.yAxisLimitsChanged.connect(
self._handle_options_view_limit_changed(y_min_changed=True,
y_max_changed=True))
self._options_view.secondaryXAxisLowerLimitChanged.connect(
self._handle_options_view_secondary_limit_changed(
x_min_changed=True))
self._options_view.secondaryXAxisUpperLimitChanged.connect(
self._handle_options_view_secondary_limit_changed(
x_max_changed=True))
self._options_view.secondaryYAxisLowerLimitChanged.connect(
self._handle_options_view_secondary_limit_changed(
y_min_changed=True))
self._options_view.secondaryYAxisUpperLimitChanged.connect(
self._handle_options_view_secondary_limit_changed(
y_max_changed=True))
self._options_view.secondaryXAxisLimitsChanged.connect(
self._handle_options_view_secondary_limit_changed(
x_min_changed=True, x_max_changed=True))
self._options_view.secondaryYAxisLimitsChanged.connect(
self._handle_options_view_secondary_limit_changed(
y_min_changed=True, y_max_changed=True))
def setLegendControl(self, legend_control):
self._legend_control = legend_control
self._legend_control.seriesUpdated.connect(self._legend_series_updated)
self._legend_control.showLegendChanged.connect(self._show_legend)
self._legend_control.seriesNameChanged.connect(
self._handle_series_name_changed)
self._legend_control.showSeriesChanged.connect(
self._handle_show_series_changed)
bind(self._legend_control, self, 'hasHiddenSeries', two_way=False)
def _legend_series_updated(self):
if self._legend is not None:
self._show_legend(self._legend_control.showLegend)
def _show_legend(self, show):
if self._legend and not show:
self._legend.remove()
self._legend = None
self.draw()
elif show:
if self._legend:
self._legend.remove()
show_series = self._legend_control.showSeries
handles = [
h for h, s in zip(self._legend_control.seriesHandles,
show_series) if s
]
names = [
n
for n, s in zip(self._legend_control.seriesNames, show_series)
if s
]
axes = (self._secondary_axes if self._secondary_axes
and self._secondary_axes.get_visible()
and self._secondary_axes.get_zorder() >
self._axes.get_zorder() else self._axes)
self._legend = self._create_legend(
axes,
handles,
names,
markerscale=self._get_legend_markerscale())
if self._get_legend_text_color() is not None:
for text in self._legend.texts:
text.set_color(self._get_legend_text_color())
self._draggable_legend = DraggableLegend(self._legend)
self.draw()
def _get_legend_markerscale(self):
return 5
def _create_legend(self, axes, handles, names, **kwargs):
return axes.legend(handles, names, **kwargs)
def _get_legend_text_color(self):
return None
def _handle_series_name_changed(self, index, series_name):
if self._legend is not None and index < len(
self._legend_control.seriesHandles):
visible_handles = [
h for h, s in zip(self._legend_control.seriesHandles,
self._legend_control.showSeries)
if s and h is not None
]
try:
legend_index = visible_handles.index(
self._legend_control.seriesHandles[index])
except ValueError:
return
if legend_index < len(self._legend.texts):
self._legend.texts[legend_index].set_text(series_name)
self.draw()
def _handle_show_series_changed(self, index, show_series):
if index < len(self._legend_control.seriesHandles):
self._set_series_visibility(
self._legend_control.seriesHandles[index], show_series)
if self._legend is not None:
self._show_legend(self._legend_control.showLegend)
else:
self.draw()
def _set_series_visibility(self, handle, visible):
if not handle:
return
if hasattr(handle, 'set_visible'):
handle.set_visible(visible)
elif hasattr(handle, 'get_children'):
for child in handle.get_children():
self._set_series_visibility(child, visible)
def _update_grid_lines(self):
show_grid_lines = False if self._options_view is None else self._options_view.showGridLines
gridline_color = self._axes.spines['bottom'].get_edgecolor()
gridline_color = gridline_color[0], gridline_color[1], gridline_color[
2], 0.5
kwargs = dict(color=gridline_color,
alpha=0.5) if show_grid_lines else {}
self._axes.grid(show_grid_lines, **kwargs)
self.draw()
def _handle_options_view_limit_changed(self,
x_min_changed=False,
x_max_changed=False,
y_min_changed=False,
y_max_changed=False):
def _():
if self._options_view is None or self._setting_axis_limits:
return
(x_min, x_max), (y_min, y_max) = (new_x_min, new_x_max), (
new_y_min, new_y_max) = self._get_xy_extents()
(x_opt_min,
x_opt_max), (y_opt_min,
y_opt_max) = self._get_options_view_xy_extents()
if x_min_changed:
new_x_min = x_opt_min
if x_max_changed:
new_x_max = x_opt_max
if y_min_changed:
new_y_min = y_opt_min
if y_max_changed:
new_y_max = y_opt_max
if [new_x_min, new_x_max, new_y_min, new_y_max
] != [x_min, x_max, y_min, y_max]:
self._xy_extents = (new_x_min, new_x_max), (new_y_min,
new_y_max)
self._set_axes_limits()
self.draw()
return _
def _get_options_view_xy_extents(self):
(x_data_min, x_data_max), (y_data_min,
y_data_max) = self._get_data_xy_extents()
x_min = x_data_min if np.isnan(
self._options_view.xAxisLowerLimit
) else self._options_view.xAxisLowerLimit
x_max = x_data_max if np.isnan(
self._options_view.xAxisUpperLimit
) else self._options_view.xAxisUpperLimit
y_min = y_data_min if np.isnan(
self._options_view.yAxisLowerLimit
) else self._options_view.yAxisLowerLimit
y_max = y_data_max if np.isnan(
self._options_view.yAxisUpperLimit
) else self._options_view.yAxisUpperLimit
return (x_min, x_max), (y_min, y_max)
def _handle_options_view_secondary_limit_changed(self,
x_min_changed=False,
x_max_changed=False,
y_min_changed=False,
y_max_changed=False):
def _():
if self._options_view is None or self._setting_axis_limits:
return
updated = False
(x_opt_min, x_opt_max), (
y_opt_min,
y_opt_max) = self._get_options_view_secondary_xy_extents()
if self._has_secondary_y_extent() and (y_min_changed
or y_max_changed):
y_min, y_max = new_y_min, new_y_max = self._get_secondary_y_extent(
)
if y_min_changed:
new_y_min = y_opt_min
if y_max_changed:
new_y_max = y_opt_max
if [new_y_min, new_y_max] != [y_min, y_max]:
self._secondary_y_extent = (new_y_min, new_y_max)
updated = True
if self._has_secondary_x_extent() and (x_min_changed
or x_max_changed):
x_min, x_max = new_x_min, new_x_max = self._get_secondary_x_extent(
)
if x_min_changed:
new_x_min = x_opt_min
if x_max_changed:
new_x_max = x_opt_max
if [new_x_min, new_x_max] != [x_min, x_max]:
self._secondary_x_extent = (new_x_min, new_x_max)
updated = True
if updated:
self._set_axes_limits()
self.draw()
return _
def _get_options_view_secondary_xy_extents(self):
x_data_min, x_data_max = self._get_data_secondary_x_extent()
y_data_min, y_data_max = self._get_data_secondary_y_extent()
x_min = x_data_min if np.isnan(
self._options_view.secondaryXAxisLowerLimit
) else self._options_view.secondaryXAxisLowerLimit
x_max = x_data_max if np.isnan(
self._options_view.secondaryXAxisUpperLimit
) else self._options_view.secondaryXAxisUpperLimit
y_min = y_data_min if np.isnan(
self._options_view.secondaryYAxisLowerLimit
) else self._options_view.secondaryYAxisLowerLimit
y_max = y_data_max if np.isnan(
self._options_view.secondaryYAxisUpperLimit
) else self._options_view.secondaryYAxisUpperLimit
return (x_min, x_max), (y_min, y_max)
def _on_data_changed(self):
self._cached_label_width_height = None
def closeEvent(self, event):
QWidget.closeEvent(self, event)
if event.isAccepted():
self._zoom_selector.onselect = self._span.onselect = self._span._select_none_handler = None
def set_divider_h_margin(self, h_margin):
h = [
Size.Fixed(h_margin[0]),
Size.Scaled(1.0),
Size.Fixed(h_margin[1])
]
self._divider.set_horizontal(h)
def set_divider_v_margin(self, v_margin):
v = [
Size.Fixed(v_margin[0]),
Size.Scaled(1.0),
Size.Fixed(v_margin[1])
]
self._divider.set_vertical(v)
@property
def x_extent_padding(self):
return self._x_extent_padding
@x_extent_padding.setter
def x_extent_padding(self, value):
self._x_extent_padding = value
@property
def y_extent_padding(self):
return self._y_extent_padding
@y_extent_padding.setter
def y_extent_padding(self, value):
self._y_extent_padding = value
def _in_interval(self, value, interval):
return interval[0] <= value <= interval[1]
def _interval_skew(self, value, interval):
return (value - interval[0]) / (interval[1] - interval[0])
def _in_x_scroll_zone(self, event):
return self._in_interval(event.x, self._axes.bbox.intervalx
) and event.y <= self._axes.bbox.intervaly[1]
def _in_y_scroll_zone(self, event):
return self._in_interval(event.y, self._axes.bbox.intervaly
) and event.x <= self._axes.bbox.intervalx[1]
def _on_scroll(self, event):
if self._secondary_axes is not None:
self._handle_scroll_secondary(event)
in_x = self._in_x_scroll_zone(event)
in_y = self._in_y_scroll_zone(event)
if in_x or in_y and event.button in ['up', 'down']:
(x_min, x_max), (y_min, y_max) = self._get_actual_xy_extents()
if (in_x and self._single_axis_zoom_enabled) or (in_x and in_y):
skew = self._zoom_skew and self._zoom_skew[0]
skew = self._interval_skew(
event.x,
self._axes.bbox.intervalx) if skew is None else skew
x_min, x_max = self._zoom(x_min, x_max, skew, event.button)
if (in_y and self._single_axis_zoom_enabled) or (in_x and in_y):
skew = self._zoom_skew and self._zoom_skew[1]
skew = self._interval_skew(
event.y,
self._axes.bbox.intervaly) if skew is None else skew
y_min, y_max = self._zoom(y_min, y_max, skew, event.button)
self._xy_extents = (x_min, x_max), (y_min, y_max)
self._set_axes_limits()
self.draw()
def _in_secondary_y_scroll_zone(self, event):
return self._in_interval(event.y, self._axes.bbox.intervaly) and \
event.x >= self._axes.bbox.intervalx[1]
def _in_secondary_x_scroll_zone(self, event):
return self._in_interval(event.x, self._axes.bbox.intervalx) and \
event.y >= self._axes.bbox.intervaly[1]
def _handle_scroll_secondary(self, event):
if self._has_secondary_y_extent():
in_secondary_y = self._in_secondary_y_scroll_zone(event)
if in_secondary_y and event.button in ['up', 'down']:
self._secondary_y_extent = self._zoom(
*self._get_secondary_y_extent(),
self._interval_skew(event.y, self._axes.bbox.intervaly),
event.button)
if self._has_secondary_x_extent():
in_secondary_x = self._in_secondary_x_scroll_zone(event)
if in_secondary_x and event.button in ['up', 'down']:
self._secondary_x_extent = self._zoom(
*self._get_secondary_x_extent(),
self._interval_skew(event.x, self._axes.bbox.intervalx),
event.button)
def _get_zoom_multiplier(self):
return 20 / 19
def _zoom(self, min_, max_, skew, direction):
zoom_multiplier = self._get_zoom_multiplier(
) if direction == 'up' else 1 / self._get_zoom_multiplier()
range_ = max_ - min_
diff = (range_ * (1 / zoom_multiplier)) - range_
max_ += diff * (1 - skew)
min_ -= diff * skew
return min_, max_
def _set_axes_limits(self):
try:
self._setting_axis_limits = True
if self._secondary_axes is not None:
self._set_secondary_axes_limits()
self._update_ticks()
(x_min, x_max), (y_min, y_max) = self._get_xy_extents()
if self._options_view is not None:
if self._options_view.x_limits:
self._options_view.setXLimits(float(x_min), float(x_max))
if self._options_view.y_limits:
self._options_view.setYLimits(float(y_min), float(y_max))
self._axes.set_xlim(*_safe_limits(x_min, x_max))
self._axes.set_ylim(*_safe_limits(y_min, y_max))
finally:
self._setting_axis_limits = False
def _set_secondary_axes_limits(self):
if self._options_view is not None:
if self._options_view.secondary_y_limits:
enabled = self._secondary_y_enabled()
secondary_y_min, secondary_y_max = self._get_secondary_y_extent(
) if enabled else (float('nan'), float('nan'))
self._options_view.setSecondaryYLimitsEnabled(enabled)
self._options_view.setSecondaryYLimits(float(secondary_y_min),
float(secondary_y_max))
if self._options_view.secondary_x_limits:
enabled = self._secondary_x_enabled()
secondary_x_min, secondary_x_max = self._get_secondary_x_extent(
) if enabled else (float('nan'), float('nan'))
self._options_view.setSecondaryXLimitsEnabled(enabled)
self._options_view.setSecondaryXLimits(float(secondary_x_min),
float(secondary_x_max))
if self._has_secondary_y_extent():
self._secondary_axes.set_ylim(*_safe_limits(
*self._get_secondary_y_extent()))
if self._has_secondary_x_extent():
self._secondary_axes.set_xlim(*_safe_limits(
*self._get_secondary_x_extent()))
def _secondary_y_enabled(self):
return True if self._secondary_axes and self._secondary_axes.get_visible(
) and self._has_secondary_y_extent() else False
def _secondary_x_enabled(self):
return True if self._secondary_axes and self._secondary_axes.get_visible(
) and self._has_secondary_x_extent() else False
def _set_axes_labels(self):
self._axes.set_xlabel(self.data.xAxisTitle)
self._axes.set_ylabel(self.data.yAxisTitle)
def _set_center(self, center):
if not all(c is not None for c in center):
center = (0, 0)
x_extent, y_extent = self._get_xy_extents()
span = x_extent[1] - x_extent[0], y_extent[1] - y_extent[0]
x_extent = center[0] - span[0] / 2, center[0] + span[0] / 2
y_extent = center[1] - span[1] / 2, center[1] + span[1] / 2
self._xy_extents = x_extent, y_extent
def _get_xy_extents(self):
if self.data is None:
return (0, 0), (0, 0)
if self._xy_extents is None:
return self._get_data_xy_extents()
return self._xy_extents
def _get_data_xy_extents(self):
if self.data is None:
return (0, 0), (0, 0)
(x_min, x_max), (y_min, y_max) = self.data.get_xy_extents()
return self._pad_extent(x_min, x_max,
self.x_extent_padding), self._pad_extent(
y_min, y_max, self.y_extent_padding)
def _has_secondary_y_extent(self):
return hasattr(self.data, 'get_secondary_y_extent')
def _get_secondary_y_extent(self):
if self._secondary_y_extent is not None:
return self._secondary_y_extent
if self.data is not None:
return self._get_data_secondary_y_extent()
return (0, 0)
def _get_data_secondary_y_extent(self):
if self.data is None:
return (0, 0)
return self._pad_extent(*self.data.get_secondary_y_extent(),
self.y_extent_padding)
def _has_secondary_x_extent(self):
return hasattr(self.data, 'get_secondary_x_extent')
def _get_secondary_x_extent(self):
if self._secondary_x_extent is not None:
return self._secondary_x_extent
if self.data is not None:
return self._get_data_secondary_x_extent()
return (0, 0)
def _get_data_secondary_x_extent(self):
if self.data is None or not hasattr(self.data,
'get_secondary_x_extent'):
return (0, 0)
return self._pad_extent(*self.data.get_secondary_x_extent(),
self.x_extent_padding)
def _get_actual_xy_extents(self):
return self._axes.get_xlim(), self._axes.get_ylim()
def _pad_extent(self, min_, max_, padding):
min_, max_ = self._zero_if_nan(min_), self._zero_if_nan(max_)
range_ = max_ - min_
return min_ - padding * range_, max_ + padding * range_
def _zoom_selected(self, start_pos, end_pos):
x_min, x_max = min(start_pos.xdata,
end_pos.xdata), max(start_pos.xdata, end_pos.xdata)
y_min, y_max = min(start_pos.ydata,
end_pos.ydata), max(start_pos.ydata, end_pos.ydata)
self._xy_extents = (x_min, x_max), (y_min, y_max)
self._set_axes_limits()
self.draw()
def _handle_span_select(self, x_min, x_max):
x_min, x_max = self._round_to_bin_width(x_min, x_max)
self._update_span_rect(x_min, x_max)
self.span = SpanModel(self, x_min, x_max)
self.draw()
def _handle_span_select_none(self):
self.span = None
def _handle_press(self, event):
if event.button == 1:
if self._is_panning:
self._pan_event = event
elif self._span.active:
self._handle_span_press(event)
def _handle_move(self, event):
if event.xdata and self._pan_event:
self._handle_pan_move(event)
elif event.xdata and any(self._span_events()):
self._handle_span_move(event)
def _handle_release(self, event):
if self._pan_event:
self._pan_event = None
elif any(self._span_events()):
self._handle_span_release(event)
def _handle_pan_move(self, event):
from_x, from_y = self._axes.transData.inverted().transform(
(self._pan_event.x, self._pan_event.y))
to_x, to_y = self._axes.transData.inverted().transform(
(event.x, event.y))
self._pan(from_x - to_x, from_y - to_y)
self._pan_event = event
def _pan(self, delta_x, delta_y):
(x_min, x_max), (y_min, y_max) = self._get_xy_extents()
self._xy_extents = (x_min + delta_x,
x_max + delta_x), (y_min + delta_y,
y_max + delta_y)
self._set_axes_limits()
self.draw()
def _span_events(self):
return self._span_center_mouse_event, self._span_left_mouse_event, self._span_right_mouse_event
def _handle_span_press(self, event):
if not event.xdata:
return
span_min, span_max = (self.span.left,
self.span.right) if self.span else (0, 0)
edge_tolerance = self._span_tolerance()
if abs(span_min - event.xdata) < edge_tolerance:
self._span.active = False
self._span_left_mouse_event = event
elif abs(span_max - event.xdata) < edge_tolerance:
self._span.active = False
self._span_right_mouse_event = event
elif span_min < event.xdata < span_max:
self._span.active = False
self._span_center_mouse_event = event
def _handle_span_move(self, event):
if not self.span:
return
x_min, x_max = self.span.left, self.span.right
last_event = next(x for x in self._span_events() if x)
diff_x = event.xdata - last_event.xdata
if self._span_center_mouse_event is not None:
self._update_span_rect(x_min + diff_x)
elif self._span_left_mouse_event is not None:
self._update_span_rect(x_min + diff_x, x_max)
elif self._span_right_mouse_event is not None:
self._update_span_rect(x_min, x_max + diff_x)
self.draw([self._span.rect])
def _handle_span_release(self, _event):
x_min = self._span.rect.get_x()
x_max = x_min + self._span.rect.get_width()
x_min, x_max = self._round_to_bin_width(x_min, x_max)
self._update_span_rect(x_min, x_max)
self.span = SpanModel(self, x_min, x_max)
self.draw()
self._span.active = True
self._span_center_mouse_event = self._span_left_mouse_event = self._span_right_mouse_event = None
def _update_span_rect(self, x_min, x_max=None):
self._span.rect.set_x(x_min)
self._span.stay_rect.set_x(x_min)
if x_max:
self._span.rect.set_width(x_max - x_min)
self._span.stay_rect.set_width(x_max - x_min)
def _round_to_bin_width(self, x_min, x_max):
return x_min, x_max
def _span_tolerance(self):
return 5
def toolEnabled(self, _tool_type):
return False
def toolAvailable(self, _tool_type):
return False
def activateTool(self, tool_type, active):
if tool_type == ToolType.zoom:
self._zoom_selector.set_active(active)
elif tool_type == ToolType.span:
if self._span.active and not active:
self._previous_span = self.span
self.span = None
for r in [self._span.rect, self._span.stay_rect]:
self._remove_artist(r)
elif not self._span.active and active:
self.span = self._previous_span
for r in [self._span.rect, self._span.stay_rect]:
self._add_artist(r)
self._span.active = active
self.draw()
elif tool_type == ToolType.pan:
self._is_panning = active
self._active_tools[tool_type] = active
def toolActive(self, tool_type):
return self._active_tools.get(tool_type, False)
def isActiveDefault(self, _tool_type):
return False
def _add_artist(self, artist):
self._axes.add_artist(artist)
self._decoration_artists.append(artist)
def _remove_artist(self, artist):
artist.remove()
if artist in self._decoration_artists:
self._decoration_artists.remove(artist)
def _handle_resize(self, _event):
self._update_ticks()
return self.draw()
def draw(self, artists=None):
if artists is None:
def _update():
for a in self._decoration_artists:
a.remove()
self._canvas.draw()
self._background_cache = self._canvas.copy_from_bbox(
self._figure.bbox)
for a in self._decoration_artists:
self._axes.add_artist(a)
self._axes.draw_artist(a)
self._canvas.update()
self._pending_draw = _update
else:
def _update():
if self._background_cache is None:
raise RuntimeError('Must run draw before drawing artists!')
self._canvas.restore_region(self._background_cache)
for a in artists:
self._axes.draw_artist(a)
self._canvas.update()
self._pending_artists_draw = _update
def _do_draw_events(self):
if self._pending_draw is not None:
self._pending_draw()
self._pending_draw = None
if self._pending_artists_draw is not None:
self._pending_artists_draw()
self._pending_artists_draw = None
if self._other_draw_events:
for draw_event in self._other_draw_events:
draw_event()
self._other_draw_events = []
def addDrawEvent(self, draw_event):
self._other_draw_events.append(draw_event)
def resetZoom(self):
self._secondary_y_extent = self._secondary_x_extent = None
self._xy_extents = None
self._set_axes_limits()
self.draw()
def _twinx(self, ylabel):
axes = self._axes.twinx()
for spine in ['top', 'left']:
axes.spines[spine].set_visible(False)
axes.set_ylabel(ylabel)
axes.set_zorder(1)
return axes
@property
def axes(self):
return self._axes
@property
def secondary_axes(self):
if self._secondary_axes is None:
self._set_secondary_axes(self._twinx(''))
return self._secondary_axes
def _set_secondary_axes(self, axes):
self._secondary_axes = axes
@staticmethod
def sizeHint():
"""function::sizeHint()
Override the default sizeHint to ensure the plot has an initial size
"""
return QSize(600, 400)
def minimumSizeHint(self):
"""function::sizeHint()
Override the default sizeHint to ensure the plot does not shrink below minimum size
"""
return self.sizeHint()
@staticmethod
def _zero_if_nan(value):
return value if not isinstance(value,
float) or not np.isnan(value) else 0
def canShowTable(self):
return hasattr(self, 'data') and self.data is not None and hasattr(
self.data, 'table')
def contextMenuEvent(self, event):
self._show_table_action.setEnabled(self.canShowTable())
self._menu.exec_(event.globalPos())
def copyToClipboard(self):
with BytesIO() as buffer:
self._figure.savefig(buffer,
facecolor=self._figure.get_facecolor())
QApplication.clipboard().setImage(
QImage.fromData(buffer.getvalue()))
def saveAsImage(self):
filename = self._file_dialog_service.get_save_filename(
self, self.tr('Portable Network Graphics (*.png)'))
if filename:
self._figure.savefig(filename,
facecolor=self._figure.get_facecolor())
def showTable(self):
if self.canShowTable():
self._table_view = TableView(None)
self._table_view.pasteEnabled = False
self._table_view.setModel(self.data.table)
self._table_view.setMinimumSize(800, 600)
self._table_view.show()
def _update_ticks(self):
if not self.data:
return
if hasattr(self.data, 'x_labels'):
step = self.data.x_tick_interval if hasattr(
self.data, 'x_tick_interval') else None
x_ticks, x_labels = self._get_labels(self.data.x_labels,
step,
horizontal=True)
self._axes.set_xticks(x_ticks)
self._axes.set_xticklabels(x_labels)
if hasattr(self.data, 'y_labels'):
step = self.data.y_tick_interval if hasattr(
self.data, 'y_tick_interval') else None
y_ticks, y_labels = self._get_labels(self.data.y_labels,
step,
horizontal=False)
self._axes.set_yticks(y_ticks)
self._axes.set_yticklabels(y_labels)
def _get_labels(self, labels, step, horizontal=True):
(x0, x1), (y0, y1) = self._get_xy_extents()
start, end = (int(x0), int(x1)) if horizontal else (int(y0), int(y1))
visible_points = end - start
if not (step and step > 0):
width, height = self._get_label_width_height(labels)
axes_bbox = self._axes.get_window_extent(
self._figure.canvas.get_renderer()).transformed(
self._figure.dpi_scale_trans.inverted())
plot_size = (axes_bbox.width if horizontal else
axes_bbox.height) * self._figure.dpi
size = (width if horizontal else height)
if plot_size == 0 or size == 0:
n_labels = 16
else:
n_labels = int(plot_size / size)
if n_labels == 0:
n_labels = 16
step = int(visible_points / n_labels) + 1
else:
step = int(step)
indexes = list(range(len(labels)))
display_labels = list(labels)
for i in indexes:
if i % step:
display_labels[i] = ''
return indexes, display_labels
def _get_label_width_height(self, labels):
if not self._cached_label_width_height:
font = MatPlotLibFont.default()
width = 0
height = 0
for label in labels:
next_width, next_height = font.get_size(
str(label), matplotlib.rcParams['font.size'],
self._figure.dpi)
width = max(width, next_width)
height = max(height, next_height)
self._cached_label_width_height = width, height
return self._cached_label_width_height
def _create_new_axes(self, nx=1, ny=1) -> LocatableAxes:
axes = LocatableAxes(self._figure, self._divider.get_position())
axes.set_axes_locator(self._divider.new_locator(nx=nx, ny=ny))
self._figure.add_axes(axes)
return axes
@staticmethod
def _create_secondary_xy_axes(figure,
divider,
nx=1,
ny=1,
visible=False,
z_order=1):
axes = LocatableAxes(figure, divider.get_position())
axes.set_axes_locator(divider.new_locator(nx=nx, ny=ny))
axes.xaxis.tick_top()
axes.xaxis.set_label_position('top')
axes.yaxis.tick_right()
axes.yaxis.set_label_position('right')
axes.patch.set_visible(visible)
axes.set_zorder(z_order)
figure.add_axes(axes)
axes.ticklabel_format(style='sci', axis='x', scilimits=(-4, 4))
axes.ticklabel_format(style='sci', axis='y', scilimits=(-4, 4))
return axes
@staticmethod
def _create_shared_axes(figure,
divider,
shared_axes,
nx=1,
ny=1,
visible=False,
z_order=1):
axes = LocatableAxes(figure,
divider.get_position(),
sharex=shared_axes,
sharey=shared_axes,
frameon=False)
axes.set_axes_locator(divider.new_locator(nx=nx, ny=ny))
for spine in axes.spines.values():
spine.set_visible(False)
for axis in axes.axis.values():
axis.set_visible(False)
axes.patch.set_visible(False)
axes.set_visible(False)
axes.set_zorder(z_order)
figure.add_axes(axes)
return axes
def delay_avg_svg(self, ttype, b64encode=True):
fig = pyplot.figure(figsize=self.FIGSIZE)
h = [Size.Fixed(1.2), Size.Scaled(1.), Size.Fixed(.2)]
v = [Size.Fixed(0.7), Size.Scaled(1.), Size.Fixed(.5)]
divider = Divider(fig, (0.0, 0.0, 1., 1.), h, v, aspect=False)
plt = Axes(fig, divider.get_position())
plt.set_axes_locator(divider.new_locator(nx=1, ny=1))
fig.add_axes(plt)
result = self.result
runinfo = result.runinfo
# ----
# The X limits are -rampupMins, runMins
# ----
plt.set_xlim(-int(runinfo['rampupMins']), int(runinfo['runMins']))
plt.axvspan(-int(runinfo['rampupMins']), 0, facecolor='0.2', alpha=0.1)
# ----
# offset the timestamps by -rampupMins so that the graph
# starts with negative minutes elapsed and switches to
# positive when the measurement begins.
# ----
offset = (int(runinfo['rampupMins'])) * 60.0
# ----
# ttype transaction delay. First get the timestamp
# and delay numbers from the result data.
# The X vector then is the sorted unique timestamps rounded
# to an interval.
# ----
interval = 10
data = numpy.array([[(int(tup[0] / interval) * interval - offset) / 60,
tup[1], tup[5]]
for tup in result.result_ttype[ttype]])
x = sorted(numpy.unique(data[:, 0]))
# ----
# The Y vector is the sums of transactions delay divided by
# the sums of the count, grouped by X.
# ----
y = []
for ts in x:
tmp = data[numpy.where(data[:, 0] == ts)]
y.append(numpy.sum(tmp[:, 2]) / (numpy.sum(tmp[:, 1]) + 0.000001))
# ----
# Plot the ttype delay and add all the decorations
# ----
plt.plot(x, y, 'r', label='Delay')
# ----
# Now do the same aggregation for the latency
# ----
data = numpy.array([[(int(tup[0] / interval) * interval - offset) / 60,
tup[1], tup[2]]
for tup in result.result_ttype[ttype]])
# ----
# The Y vector is similar by based on latency
# ----
y = []
for ts in x:
tmp = data[numpy.where(data[:, 0] == ts)]
y.append(numpy.sum(tmp[:, 2]) / (numpy.sum(tmp[:, 1]) + 0.000001))
plt.plot(x, y, 'b', label='Latency')
plt.set_title("{} Average Latency and Delay".format(ttype))
plt.set_xlabel("Elapsed Minutes")
plt.set_ylabel("Latency/Delay in ms")
plt.legend(loc='upper left')
plt.grid()
buf = io.StringIO()
pyplot.savefig(buf, format='svg')
if not b64encode:
return buf.getvalue()
return base64.b64encode(buf.getvalue().encode('utf-8')).decode('utf-8')
# # if use_alpha:
# rgba = colors.hsv_to_rgb(hsv)
# rgba = np.dstack([rgba, alpha])
# # else:
# hsv[:, :, 2] = alpha.clip(min=0.2, max=value)
# rgba_l = colors.hsv_to_rgb(hsv)
# alpha_l = np.abs(1 - alpha).clip(min=value, max=1)
# hsv[:, :, 2] = alpha_l
# rgba_lr = colors.hsv_to_rgb(hsv)
cmap = colors.ListedColormap(cmap, name='test1')
fig = plt.figure(1, figsize=(12, 8))
h = [Size.Fixed(0.), Size.Fixed(6.5)]
v = [Size.Fixed(0.5), Size.Fixed(3.25)]
win = Divider(fig, (0.1, 0.1, 0.8, 0.8), h, v, aspect=False)
ax = Axes(fig, win.get_position())
ax.set_axes_locator(win.new_locator(nx=1, ny=1))
fig.add_axes(ax)
# fig = plt.gcf()
for ii in range(1, 2):
if ii == 0:
to_plot = rgb
title = 'Model'
elif ii == 1:
to_plot = rgba
title = 'Model + Resolution (Transparency)'
elif ii == 2:
to_plot = rgba_l
title = 'Model + Resolution (Lightness)'
else:
def __init__(self,
parent,
file_dialog_service,
h_margin=(0.8, 0.1),
v_margin=(0.5, 0.15),
h_axes=[Size.Scaled(1.0)],
v_axes=[Size.Scaled(1.0)],
nx_default=1,
ny_default=1):
QWidget.__init__(self, parent)
self._file_dialog_service = file_dialog_service
self._figure = Figure()
self._canvas = FigureCanvas(self._figure)
h = [Size.Fixed(h_margin[0]), *h_axes, Size.Fixed(h_margin[1])]
v = [Size.Fixed(v_margin[0]), *v_axes, Size.Fixed(v_margin[1])]
self._divider = Divider(self._figure, (0.0, 0.0, 1.0, 1.0),
h,
v,
aspect=False)
self._axes = LocatableAxes(self._figure, self._divider.get_position())
self._axes.set_axes_locator(
self._divider.new_locator(nx=nx_default, ny=ny_default))
self._axes.set_zorder(2)
self._axes.patch.set_visible(False)
for spine in ['top', 'right']:
self._axes.spines[spine].set_visible(False)
self._figure.add_axes(self._axes)
self._canvas.setParent(self)
self._layout = QVBoxLayout(self)
self._layout.setContentsMargins(0, 0, 0, 0)
self._layout.addWidget(self._canvas)
self.setLayout(self._layout)
self._figure.canvas.mpl_connect('scroll_event', self._on_scroll)
self._xy_extents = None
self._background_cache = None
self._decoration_artists = []
self._is_panning = False
self._zoom_selector = _RectangleSelector(self._axes,
self._zoom_selected)
self._zoom_selector.set_active(False)
self._x_extent_padding = 0.01
self._y_extent_padding = 0.01
self._axes.ticklabel_format(style='sci', axis='x', scilimits=(-4, 4))
self._axes.ticklabel_format(style='sci', axis='y', scilimits=(-4, 4))
self._active_tools = {}
self._span = _SpanSeletor(self._axes,
self._handle_span_select,
'horizontal',
rectprops=dict(alpha=0.2,
facecolor='red',
edgecolor='k'),
span_stays=True)
self._span.set_on_select_none(self._handle_span_select_none)
self.span = self._previous_span = None
self._span_center_mouse_event = None
self._span_left_mouse_event = None
self._span_right_mouse_event = None
self._figure.canvas.mpl_connect('button_press_event',
self._handle_press)
self._figure.canvas.mpl_connect('motion_notify_event',
self._handle_move)
self._figure.canvas.mpl_connect('button_release_event',
self._handle_release)
self._figure.canvas.mpl_connect('resize_event', self._handle_resize)
self.activateTool(ToolType.span, self.isActiveDefault(ToolType.span))
self._pan_event = None
self._pending_draw = None
self._pending_artists_draw = None
self._other_draw_events = []
self._draw_timer = QTimer(self)
self._draw_timer.timeout.connect(self._do_draw_events)
self._draw_timer.start(20)
self._zoom_skew = None
self._menu = QMenu(self)
self._copy_image_action = QAction(self.tr('Copy To Clipboard'), self)
self._copy_image_action.triggered.connect(self.copyToClipboard)
self._copy_image_action.setShortcuts(QKeySequence.Copy)
self._save_image_action = QAction(self.tr('Save As Image'), self)
self._save_image_action.triggered.connect(self.saveAsImage)
self._show_table_action = QAction(self.tr('Show Table'), self)
self._show_table_action.triggered.connect(self.showTable)
self._menu.addAction(self._copy_image_action)
self._menu.addAction(self._save_image_action)
self._menu.addAction(self._show_table_action)
self.addAction(self._copy_image_action)
self._table_view = None
self._single_axis_zoom_enabled = True
self._cached_label_width_height = None
if hasattr(type(self), 'dataChanged'):
self.dataChanged.connect(self._on_data_changed)
self._options_view = None
self._secondary_axes = self._secondary_y_extent = self._secondary_x_extent = None
self._legend = None
self._draggable_legend = None
self._setting_axis_limits = False
self.hasHiddenSeries = False
data = extract_csvs(stacked_boxplot.visualization, './data/temp/csv')
level_4 = data[4]
# Filters the level 4 data to CD and UC
IBD_level_4 = level_4.loc[level_4['dx'].isin(["CD", "UC"])]
IBD_level_4 = IBD_level_4.drop(columns=metadata_columns)
IBD_level_4 = IBD_level_4.set_index('index')
# Normalise the data around 0
standardised = (IBD_level_4 - IBD_level_4.mean()) / IBD_level_4.std()
# sets the sizing so as much of the label can be shown as possible
fig = plt.figure(figsize=(11.7, 8.27))
h = [Size.Fixed(6.), Size.Scaled(.5), Size.Fixed(.2)]
v = [Size.Fixed(0.7), Size.Scaled(.5), Size.Fixed(.5)]
divider = Divider(fig, (0, 0, 1, 1), h, v, aspect=False)
ax = fig.add_axes(divider.get_position(),
axes_locator=divider.new_locator(nx=1, ny=1))
# Plots the relative frequency
sns.boxplot(y="variable", x="value", data=pd.melt(standardised), showfliers=False, width=.6, ax=ax)
ax.xaxis.grid(True)
ax.set(ylabel="Bacteria", xlabel="Relative Abundance",
title="Relative Abundance for IBD for taxa at level 4")
sns.despine(trim=True, left=True)
plt.savefig(out_individual_boxplot)
this_experiment = {
"_id": experiment_id,
"parent": parent_name,
"stage": CURRENT_STAGE,
ax.tick_params(bottom=False, labelbottom=False,
left=False, labelleft=False)
fig = plt.figure(figsize=(12, 6))
sfs = fig.subfigures(1, 2)
sfs[0].suptitle("Fixed axes sizes, fixed paddings")
# Sizes are in inches.
horiz = [Size.Fixed(1.), Size.Fixed(.5), Size.Fixed(1.5), Size.Fixed(.5)]
vert = [Size.Fixed(1.5), Size.Fixed(.5), Size.Fixed(1.)]
rect = (0.1, 0.1, 0.8, 0.8)
# Divide the axes rectangle into a grid with sizes specified by horiz * vert.
div = Divider(sfs[0], rect, horiz, vert, aspect=False)
# The rect parameter will actually be ignored and overridden by axes_locator.
ax1 = sfs[0].add_axes(rect, axes_locator=div.new_locator(nx=0, ny=0))
label_axes(ax1, "nx=0, ny=0")
ax2 = sfs[0].add_axes(rect, axes_locator=div.new_locator(nx=0, ny=2))
label_axes(ax2, "nx=0, ny=2")
ax3 = sfs[0].add_axes(rect, axes_locator=div.new_locator(nx=2, ny=2))
label_axes(ax3, "nx=2, ny=2")
ax4 = sfs[0].add_axes(rect, axes_locator=div.new_locator(nx=2, nx1=4, ny=0))
label_axes(ax4, "nx=2, nx1=4, ny=0")
sfs[1].suptitle("Scalable axes sizes, fixed paddings")
# Fixed sizes are in inches, scaled sizes are relative.
horiz = [Size.Scaled(1.5), Size.Fixed(.5), Size.Scaled(1.), Size.Scaled(.5)]
