def gen_collection(self, ax):
return mplc.CircleCollection(transOffset=ax.transData,
offsets=self.offsets,
sizes=self.sizes,
edgecolor=self.edgecolor,
facecolor=self.facecolor,
zorder=self.zorder)
def _draw_png_matplotlib(
X,
I,
J,
filepath,
noderadius=0.2,
linkwidth=0.05,
width=1000,
border=50,
nodeopacity=1,
linkopacity=1,
):
import matplotlib.pyplot as plt
import matplotlib.collections as mc
fig = plt.figure(figsize=(width, width))
ax = plt.axes()
ax.set_xlim(min(X[:, 0]), max(X[:, 0]))
ax.set_ylim(min(X[:, 1]), max(X[:, 1]))
ax.axis("off")
ax.set_aspect("equal", "box")
# convert input data widths to display coordinates
x_display_min, y_display_min = ax.transData.inverted().transform((0, 0))
noderadius_disp, linkwidth_disp = ax.transData.transform(
(x_display_min + noderadius, y_display_min + linkwidth))
links = zip((X[i] for i in I), (X[j] for j in J))
lc = mc.LineCollection(links,
linewidths=linkwidth_disp,
colors=(0, 0, 0, linkopacity))
ax.add_collection(lc)
cc = mc.CircleCollection(
np.full(len(X), noderadius_disp * noderadius_disp),
offsets=X,
transOffset=ax.transData,
linewidths=0,
facecolors=(0, 0, 0, nodeopacity),
)
ax.add_collection(cc)
border_data, _ = ax.transLimits.transform((border / width, 0))
ax.set_xlim(
min(X[:, 0]) - noderadius - border_data,
max(X[:, 0]) + noderadius + border_data)
ax.set_ylim(
min(X[:, 1]) - noderadius - border_data,
max(X[:, 1]) + noderadius + border_data)
fig.savefig(
filepath,
dpi=1,
bbox_inches="tight",
format="png",
transparent=True,
origin="upper",
)
def test_set_offsets_late():
identity = mtransforms.IdentityTransform()
sizes = [2]
null = mcollections.CircleCollection(sizes=sizes)
init = mcollections.CircleCollection(sizes=sizes, offsets=(10, 10))
late = mcollections.CircleCollection(sizes=sizes)
late.set_offsets((10, 10))
# Bbox.__eq__ doesn't compare bounds
null_bounds = null.get_datalim(identity).bounds
init_bounds = init.get_datalim(identity).bounds
late_bounds = late.get_datalim(identity).bounds
# offsets and transform are applied when set after initialization
assert null_bounds != init_bounds
assert init_bounds == late_bounds
def LoadPlotandSave(filename, unknown=False, flip=False, legend=False):
a = np.load(filename)
newfilename = filename
recon = a['ReconstructedObject']
recon = recon[4:251, 4:251]
recon_sorted = recon.copy().flatten()
recon_sorted.sort()
recon[recon > recon_sorted[-100]] = recon_sorted[-100]
recon = np.fliplr(recon)
cmaps = ['inferno']
i = 0
plt.imshow(recon**.5, cmap=cmaps[i])
plt.show()
imsave(newfilename[:-4] + '_Object.png', recon, cmap=cmaps[i])
if unknown:
Trajectory = a['Trajectory']
print('Test')
W_np = a['W_np']
xpos = a['xpos']
zpos = a['zpos']
W_np_onehot = np.zeros((W_np.shape[0], 33 * 33))
for i in range(W_np.shape[0]):
W_np_onehot[i, np.argmax(W_np[i])] = 1
W_np_onehot = np.reshape(W_np_onehot, (W_np.shape[0], 33, 33))
W_np_zs = np.array(
[np.nonzero(W_np_onehot[i])[0] for i in range(W_np.shape[0])])
W_np_xs = np.array(
[np.nonzero(W_np_onehot[i])[1] for i in range(W_np.shape[0])])
if flip:
W_np_xs = 32 - W_np_xs
import matplotlib.collections as collections
fig = plt.figure(num=None,
figsize=(4, 4),
dpi=200,
facecolor='w',
edgecolor='k')
ax = fig.add_subplot(1, 1, 1)
gt_call = plt.scatter(-zpos, xpos, s=10, c=(0, 0, 0))
for i in range(W_np.shape[0]):
min_alpha = .2
max_alpha = .8
alpha = min_alpha + (max_alpha - min_alpha) * i / W_np.shape[0]
c = ((1 - i / W_np.shape[0]), 0, (i / W_np.shape[0]), alpha)
if i == 0:
init_call = ax.scatter(-W_np_zs[i] / 32. * .15,
W_np_xs[i] / 32.,
s=100,
c=c) #, alpha=alpha)
else:
final_call = ax.scatter(-W_np_zs[i] / 32. * .15,
W_np_xs[i] / 32.,
s=100,
c=c) #, alpha=alpha)
alpha_start = min_alpha
alpha_mid = min_alpha + (max_alpha - min_alpha) * np.floor(
W_np.shape[0] / 2) / W_np.shape[0]
alpha_end = min_alpha + (max_alpha - min_alpha) * (W_np.shape[0] -
1) / W_np.shape[0]
c_start = ((1 - 0 / W_np.shape[0]), 0, (0 / W_np.shape[0]),
alpha_start)
c_mid = ((1 - np.floor(W_np.shape[0] / 2) / W_np.shape[0]), 0,
np.floor(W_np.shape[0] / 2) / W_np.shape[0], alpha_mid)
c_end = ((1 - (W_np.shape[0] - 1) / W_np.shape[0]), 0,
((W_np.shape[0] - 1) / W_np.shape[0]), alpha_end)
circles = collections.CircleCollection(
sizes=[100, 100, 100], facecolors=[c_start, c_mid, c_end])
circles.set_alpha(.5)
frame1 = plt.gca()
frame1.axes.get_xaxis().set_visible(False)
frame1.axes.get_yaxis().set_visible(False)
plt.savefig(newfilename[:-4] + '_Trajectory.png', bbox_inches="tight")
if legend:
leg = ax.legend((gt_call, circles), ('Truth', 'Estimate'),
fontsize='xx-large',
scatterpoints=3,
scatteryoffsets=[.5],
handlelength=2)
plt.savefig(newfilename[:-4] + '_Trajectory_wLegend.png',
bbox_inches="tight")
plt.show()
data_text_file.write(", ")
data_text_file.write(str(totalcolors[item]))
data_text_file.write('\n')
data_text_file.close()
# make the figure!
fig = plt.figure()
ax = fig.add_subplot(111, xlim=(-80,80), ylim=(-80,80))
# point sizes for our circles? point size = 82, for 82 fibres
#pointsizes = [17.253]*82*num
pointsizes = [82]*82*num
# make a collection of circles
col = collections.CircleCollection(sizes=pointsizes, offsets=just_coordinates,
transOffset=ax.transData)
trans = transforms.Affine2D().scale(fig.dpi/72.0) # one point is 1/72 inches
col.set_transform(trans) # the points to pixels transform (from example)
ax.add_collection(col, autolim=True)
ax.autoscale_view()
# our colormap will be 'hot' in reverse, with outliers (-100) in green (but only if we're plotting line data)
cust_cm = cm.hot_r
cust_cm.set_bad('gray', -50) # -100 here is just the 'alpha' value for the colour, it isn't the outlier value
col.set_cmap(cust_cm)
col.set_norm(matplotlib.colors.Normalize())
col.set_edgecolors('black') # edge colours are an off-black hue 262626
# make a masked array from the data
if data_type != 'c':
j += 1
ax = plt.gca()
format_ax(ax, "Degree", "Conservatinon score")
plt.plot(range(xlim + 1), [0.5] * (xlim + 1),
linewidth=3,
c='grey',
linestyle='-')
#plt.plot(range(xlim), [0.25]*xlim, linewidth=2, c='grey', linestyle='-')
network_patch = []
if len(network_names) > 1:
for row in patch_colors:
network_patch.append(
collections.CircleCollection([800] * len(row),
facecolor=row,
edgecolor='none'))
else: #single network, no need to show color circles
network_patch.append(
collections.CircleCollection([800],
facecolor='none',
edgecolor='none'))
#---------------------------------------------------
patch_colors = [x for x in zip(*patch_colors)]
#---------------------------------------------------
k = 0
for row in patch_colors:
patch_entries.append(
collections.CircleCollection([200] * len(row),
facecolor=row,
