def get_dataset_color(dataset,depth=None):
"""Set the colors to ensure a uniform scheme for each dataset """
dataset=string.lower(dataset)
d={}
d["dai"]=cm.Blues(.5)
d["tree"]=cm.summer(.3)
d["cru"]=cm.Blues(.9)
#models
d["picontrol"]=cm.Purples(.8)
d["h85"]="k"
d["tree_noise"]=cm.PiYG(.2)
#Soil moisture
d["merra2"]={}
d["merra2"]["30cm"]=cm.copper(.3)
d["merra2"]["2m"]=cm.copper(.3)
d["gleam"]={}
d["gleam"]["30cm"]=cm.Reds(.3)
d["gleam"]["2m"]=cm.Reds(.7)
if depth is None:
return d[dataset]
else:
return d[dataset][depth]
def get_color(self, watson, gene_type):
colors = {
"Verified": cm.Blues(0.7),
"Putative": cm.Blues(0.35),
"Dubious": "#898888"
}
if not watson:
colors['Verified'] = cm.Reds(0.5)
colors['Putative'] = cm.Reds(0.3)
colors['Uncharacterized'] = colors['Putative']
color = colors[gene_type]
return color
def NatureRevisions_Figure3(D,start_year=2019):
plt.subplot(311)
Plotting.time_plot(D.ALL.get_noise(),color=get_dataset_color("tree"),label="Pre-industrial Noise",lw=1)
Plotting.time_plot(D.ALL.projection(time=('1850-1-1','1975-12-31')),c="k",lw=1)
plt.ylabel("Projection (temporal amplitude)",fontsize=8)
plt.xlabel("Year")
plt.legend()
plt.title("(a)")#: Global Drought Atlas Projection Onto Fingerprint",fontsize=8)
plt.subplot(312)
t1900 = cdtime.comptime(1900,7,1)
times = np.arange(1,201)
likely=stats.norm.interval(.66)[1]
vlikely=stats.norm.interval(.90)[1]
certain=stats.norm.interval(.99)[1]
plt.axhline(likely,lw=1,color=cm.Reds(.33),label="Likely",alpha=.5)
plt.axhline(vlikely,lw=1,color=cm.Reds(.66),label="Very Likely",alpha=.5)
plt.axhline(certain,lw=1,color=cm.Reds(.99),label="Virtually Certain",alpha=.5)
D.ALL.time_of_emergence(t1900,times=times,color="k",lw=3)
pdsi_SN_figure(D,cdtime.comptime(1900,1,1),use_dai=True)
plt.title("(b)")#: Model-predicted time of emergence",fontsize=8)
plt.subplot(313)
hist_start = cdtime.comptime(1900,1,1)
times = np.arange(10,2100-start_year)
for X in ["ALL","ANZDA","MADA","MXDA","NADA","OWDA"]:
getattr(D,X).time_of_emergence(cdtime.comptime(start_year,1,1),times=times,color=colorregions(X),uncertainty="shade")
certain=stats.norm.interval(.99)[1]
plt.axhline(certain,lw=1,color=cm.Reds(.99),label="Virtually Certain", alpha=.5)
plt.title("(c)")#: Time of Emergence (assuming "+str(start_year)+" start)",fontsize=8)
ax1,ax2,ax3=plt.gcf().axes
ax2.set_xlim(1900,2055)
ax2.set_ylim(-3,7)
for ax in [ax1,ax2,ax3]:
ax.set_xlabel(ax.get_xlabel(),fontsize=8)
ax.set_ylabel(ax.get_ylabel(),fontsize=8)
ax3.set_xlim(start_year+10,start_year+55)
ax2.legend(fontsize=6)
ax3.legend(fontsize=6)
ax1.legend(fontsize=6)
for ax in plt.gcf().axes:
plt.setp(ax.get_xticklabels(),fontsize=6)
plt.setp(ax.get_yticklabels(),fontsize=6)
plt.setp(ax.xaxis.get_label(),fontsize=6)
plt.setp(ax.yaxis.get_label(),fontsize=6)
def plot_seed_and_gen(seedhist, genhist, figname='fig.png'):
# plot all histograms in seedhist (data), and genhist (generated)
# input:
# - datahist, genhist: numpy arrays of shape (nhists,nbins)
# - figname: name of figure to plot
# make sure that figname contains absolute path
figname = os.path.abspath(figname)
nresamp = int(genhist.shape[0] / seedhist.shape[0])
# data
plt.figure()
gen_colors = [cm.viridis(i) for i in np.linspace(0, 1, len(genhist))]
seed_colors = [cm.Reds(i) for i in np.linspace(0, 1, len(seedhist))]
for i in range(len(genhist)):
plt.plot(genhist[i, :], color=gen_colors[i])
for i in range(len(seedhist)):
plt.plot(seedhist[i, :], color='r', label='seed')
plt.title('seed and resampled histograms')
plt.legend()
plt.savefig(figname.split('.')[0] + '_show.png')
plt.close()
if nresamp != genhist.shape[0]:
plt.figure()
for i in range(len(seedhist)):
for j in range(i * nresamp, (i + 1) * nresamp):
plt.plot(genhist[j, :], color=gen_colors[j])
plt.plot(seedhist[i, :], color='r', label='seed')
plt.title('seed and resampled histograms')
plt.legend()
plt.savefig(figname.split('.')[0] + '_show' + str(i) + '.png')
plt.close()
def test_illustris():
zs = np.linspace(0.,3.,4)[:1]
ms = np.geomspace(1e8,1e16,1000)
ks = np.geomspace(1e-2,30,1001)
hcos = hmvec.HaloModel(zs,ks,ms=ms,halofit=None,mdef='vir',nfw_numeric=False)
hcos.add_battaglia_profile("electron",family="AGN",xmax=50,nxs=30000)
pee = hcos.get_power("electron")
pnn = hcos.get_power("nfw")
pne = hcos.get_power("nfw","electron")
p1 = hcos.total_matter_power_spectrum(pnn,pne,pee)
p0 = pnn
h = hcos.h
from matplotlib import cm
pl = io.Plotter(xyscale='loglin',xlabel='$k$ (h/Mpc)',ylabel='$\\Delta P / P$')
for i in range(zs.size):
pl.add(ks/h,p1[i]/p0[i],color=cm.Reds(np.linspace(0.3,0.95,zs.size)[::-1][i]),label='hmvec + Battaglia')
ok,od = np.loadtxt("data/schneider_horizon_agn.csv",delimiter=',',unpack=True)
pl.add(ok,od,lw=2,color='k',label='Horizon AGN')
ok,od = np.loadtxt("data/schneider_owls.csv",delimiter=',',unpack=True)
pl.add(ok,od,lw=2,color='k',ls='--',label='OWLS')
pl.vline(x=10.)
pl.hline(y=1.)
pl._ax.set_ylim(0.68,1.04)
pl._ax.set_xlim(0.08,25)
pl.done("illustris_comp.png")
def plot_single_trajectory(t, ts, ax, thr=0.3):
# plot absolute
from matplotlib import cm
ax[0].set_ylim(-5, 5000) #np.round((np.max(ts[2])/1000)+1)*1000)
lineages = [['1.p', '1.pp', '1.ppp'], ['4.a', '4.aa', '4.aaa']]
col = np.array([
np.array([
cm.Blues(int(i))[:3]
for i in (np.arange(len(lineages[0])) * 254. /
(len(lineages[0]) - 1) / 254.) * 127 + 127
]),
np.array([
cm.Reds(int(i))[:3]
for i in (np.arange(len(lineages[0])) * 254. /
(len(lineages[0]) - 1) / 254.) * 127 + 127
])
])
for c in [0, 1]:
for j in [0, 1, 2]:
ax[0].plot(t[j] / 60., ts[j][:, c], '-', color=col[c, j], lw=2)
# plot ratio
col = 'kcm'
diff_D = []
for j in [0, 1, 2]:
diff_D.append(
(ts[j][:, 0] - ts[j][:, 1]) / (ts[j][:, 0] + ts[j][:, 1]))
ax[1].plot(t[j] / 60., diff_D[j], '-' + col[j], lw=2)
# get T_decision
(AC_id, T_dec, ind) = get_T_decision(t, ts, 0.3)
# and plot in figure
if len(ind) > 0:
ax[1].plot(t[ind[0]][ind[1]] / 60., diff_D[ind[0]][ind[1]], 'ok')
def scale_colors(sizes, shapes):
"""
Scales colors so they aren't all faded out. Returns R/G/B scales.
:param sizes: List of sizes
:param shapes: List of shapes
:return: Colormap object
"""
size_set = sorted(list(set(sizes)))
linspace = np.linspace(0.2, 1, len(size_set))
redmap = cm.Reds(linspace)
greenmap = cm.Greens(linspace)
bluemap = cm.Blues(linspace)
colors = []
for size, shape in zip(sizes, shapes):
if shape == "icosahedron":
# Red
colors.append(redmap[size_set.index(size)])
elif shape == "elongated-pentagonal-bipyramid":
# Green
colors.append(greenmap[size_set.index(size)])
elif shape == "cuboctahedron":
# Blue
colors.append(bluemap[size_set.index(size)])
else:
raise ValueError
return colors
def plot_figure(self, x_labels, y_vals):
"""
Creates the plot with the given x and y values.
Also sets the visual params.
:param x_labels:
names of players (used for labels)
:param y_vals:
values of ownership.
:return:
"""
width = 0.35
x_vals = range(self.ncols)
for i in range(self.ncols):
color_val = y_vals[i] / 100.0 + 0.4
if color_val > 1.0:
color_val = 1.0
self.axes.bar(x_vals[i] + width,
y_vals[i],
width=width,
color=cm.Reds(color_val))
# Set the visual options of the plots
self.axes.set_xticks([x + width * 3 / 2 for x in x_vals])
self.axes.set_xticklabels(x_labels, rotation=90, size=7)
self.axes.set_yticks(range(0, 110, 10))
self.axes.tick_params(axis='y', labelsize=8)
self.axes.set_title(self.position, fontsize=10)
self.axes.set_axis_bgcolor('#242426')
self.axes.grid(axis='y', color='w', linestyle='-')
self.axes.set_axisbelow(True)
def get_strand_colors(num_times=6):
# colors
color_offset = 2
N = num_times + color_offset
blues = map(lambda x: cm.Blues(float(x) / (N), 1), range(color_offset, N))
reds = map(lambda x: cm.Reds(float(x) / (N), 1), range(color_offset, N))
return reds, blues
def get_ib_config():
nodes = [4, 8, 16, 32]
fpaths, tags, legends, colors = [], [], [], []
ps_ib_fpath = 'results_dir/out_files/{tag}out_r{r}_n{n}.csv'
ps_ib_tags = [
'SIMPLE-PS-SGD-4IB', 'SIMPLE-PS-SGD-8IB', 'SIMPLE-PS-SGD-16IB',
'SIMPLE-PS-SGD-32IB-4'
]
ps_ib_legends = [
'SGP 4 nodes', 'SGP 8 nodes', 'SGP 16 nodes', 'SGP 32 nodes'
]
ps_ib_colors = [
cm.Blues(x) for x in np.linspace(0.3, 0.8, len(ps_ib_tags))
]
fpaths.append(ps_ib_fpath)
tags.append(ps_ib_tags)
legends.append(ps_ib_legends)
colors.append(ps_ib_colors)
ar_ib_fpath = 'results_dir/out_files/{tag}out_r{r}_n{n}.csv'
ar_ib_tags = [
'AR-DPSGD-CPUCOMM-4IB-SCRATCh', 'AR-DPSGD-CPUCOMM-8IB-SCRATCh',
'AR-DPSGD-CPUCOMM-16IB-SCRATCh', 'AR-DPSGD-CPUCOMM-32IB-SCRATCH'
]
ar_ib_legends = [
'AR-SGD 4 nodes', 'AR-SGD 8 nodes', 'AR-SGD 16 nodes',
'AR-SGD 32 nodes'
]
ar_ib_colors = [cm.Reds(x) for x in np.linspace(0.3, 0.8, len(ar_ib_tags))]
fpaths.append(ar_ib_fpath)
tags.append(ar_ib_tags)
legends.append(ar_ib_legends)
colors.append(ar_ib_colors)
return nodes, fpaths, tags, legends, colors
def test_illustris():
zs = np.linspace(0., 3., 4)
ms = np.geomspace(1e8, 1e16, 1000)
ks = np.geomspace(1e-2, 30, 1001)
hcos = hmvec.HaloModel(zs,
ks,
ms=ms,
halofit=None,
mdef='vir',
nfw_numeric=False)
hcos.add_battaglia_profile("electron", family="AGN", xmax=50, nxs=30000)
pee = hcos.get_power("electron")
pnn = hcos.get_power("nfw")
pne = hcos.get_power("nfw", "electron")
p1 = hcos.total_matter_power_spectrum(pnn, pne, pee)
p0 = pnn
h = hcos.h
from matplotlib import cm
pl = io.Plotter(xyscale='loglin',
xlabel='$k$ (h/Mpc)',
ylabel='$\\Delta P / P$')
for i in range(zs.size):
pl.add(ks / h,
p1[i] / p0[i],
color=cm.Reds(np.linspace(0.3, 0.95, zs.size)[i]))
pl.vline(x=10.)
pl.hline(y=1.)
pl._ax.set_ylim(0.68, 1.04)
pl._ax.set_xlim(0.08, 25)
pl.done("illustris_comp.png")
def da_colors(typ):
d = {}
d["h85"] = cm.Oranges(.8) #cm.Dark2(0.)
d["piC"] = cm.Greens(.7) #cm.Dark2(.2)
d["gpcp"] = cm.Purples(.5) #cm.Dark2(.4)
d["cmap"] = cm.Reds(.8)
d["precl"] = cm.Purples(.9)
return d[typ]
def threeColorScales(number_of_lines, start=0.2, stop=1.0):
cm_subsection = np.linspace(start, stop, number_of_lines)
colorsBlue = [cm.Blues(x) for x in cm_subsection]
colorsRed = [cm.Reds(x) for x in cm_subsection]
colorsGreen = [cm.Greens(x) for x in cm_subsection]
allColors = [colorsBlue, colorsRed, colorsGreen]
return allColors
def highlightBackProp(image, model2):
#steering_angle = float(model.predict(image[None, :, :, :], batch_size=1))
# print(image.shape)
#image = cv2.resize(image, (256, 256) )
oldimage = image
#image = cv2.resize(image, (200, 66) )
# transpose if model is other way
count, h, w, ch = model2.inputs[0].get_shape()
ih, iw, ich = image.shape
if h == ich and ch == ih:
image = image.transpose()
#print(image.shape)
m1d = model2.predict(image[None, :, :, :], batch_size=1)
#print(m1d.shape)
m1d = np.squeeze(m1d, axis=0)
m1d = np.squeeze(m1d, axis=2)
#m1d = cv2.resize(image, (120, 160) )
#m1d=np.resize(m1d,(120,160))
#print(m1d.shape)
#print(m1d)
#plt.hist(m1d[::-1])
#plt.show()
#print(m1d.max())
#print(m1d.min())
o2 = overlay = Image.fromarray(cm.Reds(m1d / m1d.max(), bytes=True))
#o2= o2.convert("RGB")
#return o2
#plt.imshow(o2);
#plt.show();
pixeldata = list(overlay.getdata())
for i, pixel in enumerate(pixeldata):
if almostEquals(pixel[:3], (255, 255, 255)):
pixeldata[i] = (255, 255, 255, 0)
else:
pixeldata[i] = (pixel[0], pixel[1], pixel[2], 128)
overlay.putdata(pixeldata)
#obig= cv2.resize(overlay, (320, 160) )
carimg = Image.fromarray(np.uint8(image))
#carimg = Image.fromarray(np.uint8(oldimage))
carimg = carimg.convert("RGBA")
new_img2 = Image.alpha_composite(carimg, overlay)
new_img2 = new_img2.convert("RGB")
o2 = o2.convert("RGB")
#plt.imshow(o2);
#plt.show();
return np.array(new_img2)
def get_eth_config():
nodes = [4, 8, 16, 32]
fpaths, tags, legends, colors = [], [], [], []
ar_eth_fpath = 'results_dir/out_files/{tag}out_r{r}_n{n}.csv'
ar_eth_tags = [
'AR-DPSGD-CPUCOMM-4ETH-SCRATCH', 'AR-DPSGD-CPUCOMM-8ETH-SCRATCH',
'AR-DPSGD-CPUCOMM-16ETH-SCRATCH', 'AR-DPSGD-CPUCOMM-32ETH-SCRATCH'
]
ar_eth_legends = [
'AR-SGD 4 nodes', 'AR-SGD 8 nodes', 'AR-SGD 16 nodes',
'AR-SGD 32 nodes'
]
ar_eth_colors = [
cm.Reds(x) for x in np.linspace(0.3, 0.8, len(ar_eth_tags))
]
fpaths.append(ar_eth_fpath)
tags.append(ar_eth_tags)
legends.append(ar_eth_legends)
colors.append(ar_eth_colors)
ds_eth_fpath = 'results_dir/out_files/{tag}out_r{r}_n{n}.csv'
ds_eth_tags = [
'SDS-SGD-4ETH', 'SDS-SGD-8ETH', 'SDS-SGD-16ETH', 'SDS-SGD-32ETH'
]
ds_eth_legends = [
'D-PSGD 4 nodes', 'D-PSGD 8 nodes', 'D-PSGD 16 nodes',
'D-PSGD 32 nodes'
]
ds_eth_colors = [
cm.Greens(x) for x in np.linspace(0.3, 0.8, len(ds_eth_tags))
]
fpaths.append(ds_eth_fpath)
tags.append(ds_eth_tags)
legends.append(ds_eth_legends)
colors.append(ds_eth_colors)
ps_eth_fpath = 'results_dir/out_files/{tag}out_r{r}_n{n}.csv'
ps_eth_tags = [
'PS-SGD-4ETH-CHORD', 'PS-SGD-8ETH-CHORD', 'PS-SGD-16ETH-CHORD',
'PS-SGD-32ETH-SCRATCH-CHORD'
]
ps_eth_legends = [
'SGP 4 nodes', 'SGP 8 nodes', 'SGP 16 nodes', 'SGP 32 nodes'
]
ps_eth_colors = [
cm.Blues(x) for x in np.linspace(0.3, 0.8, len(ps_eth_tags))
]
fpaths.append(ps_eth_fpath)
tags.append(ps_eth_tags)
legends.append(ps_eth_legends)
colors.append(ps_eth_colors)
# return nodes, fpaths[::-1], tags[::-1], legends[::-1], colors[::-1]
return nodes, fpaths, tags, legends, colors
def onclick(self, event):
if event.inaxes == self.ax:
self.xcoords.append(event.xdata)
self.ycoords.append(event.ydata)
xlim0, xlim1 = self.ax.get_xlim()
if len(self.ycoords) == 2:
# set values for horizontal lines
self.horizontal_line1.set_ydata(self.ycoords[0])
self.horizontal_line2.set_ydata(self.ycoords[1])
# set text values with y values
self.text1.set_text("{0:.2f}".format(self.ycoords[0]))
self.text1.set_position((xlim0, self.ycoords[0]))
self.text2.set_text("{0:.2f}".format(self.ycoords[1]))
self.text2.set_position((xlim0, self.ycoords[1]))
# fill between with axhspan
self.hspan.set_xy([[0, self.ycoords[0]], [0, self.ycoords[1]],
[1, self.ycoords[1]], [1, self.ycoords[0]]])
for i in range(len(self.mean)):
prob_over_max_value = 1 - \
st.norm.cdf(max(self.ycoords),
self.mean[i], self.confint[i])
prob_under_min_value = st.norm.cdf(min(self.ycoords),
self.mean[i],
self.confint[i])
between_prob = 1 - \
(prob_over_max_value + prob_under_min_value)
if np.abs(between_prob < 0.1):
between_prob = 0
if np.abs(prob_over_max_value < 0.001):
prob_over_max_value = 0
if np.abs(prob_under_min_value < 0.001):
prob_under_min_value = 0
# print('[{}] PUMaxV: {} POMinV: {} Between probabilities: {}'.format(
# i, prob_over_max_value, prob_under_min_value, between_prob))
self.diff.append(round(between_prob, 3))
self.ax.bar(self.values,
self.mean,
yerr=[self.confint, self.confint],
edgecolor='black',
color=cm.Reds(tuple(self.diff)))
self.fig.canvas.draw()
# print(self.diff)
# reset coordinates
self.xcoords = []
self.ycoords = []
self.diff = []
def get_colors(color_c=3, color_step=100):
cmap_colors = np.vstack((
cm.Oranges(np.linspace(0.4, 1, color_step)),
cm.Reds(np.linspace(0.4, 1, color_step)),
cm.Greys(np.linspace(0.4, 1, color_step)),
cm.Purples(np.linspace(0.4, 1, color_step)),
cm.Blues(np.linspace(0.4, 1, color_step)),
cm.Greens(np.linspace(0.4, 1, color_step)),
cm.pink(np.linspace(0.4, 1, color_step)),
cm.copper(np.linspace(0.4, 1, color_step)),
))
return cmap_colors[np.arange(color_c * color_step) % (color_step * 8)]
def to_heatmap(gcam, start_r, end_r, color='red'):
if start_r != -1 and end_r != -1:
gcam[0:start_r, ...] = 0
gcam[end_r:, ...] = 0
alpha = gcam[..., None] * PROB_WEIGHT
alpha[alpha > 1.0] = 1.0
if color == 'red':
cmap = cm.Reds(gcam)[..., :3] * 255.0
else:
cmap = cm.Blues(gcam)[..., :3] * 255.0
cmap = cmap[..., ::-1]
cmap = cmap.astype(np.float)
return cmap, alpha
def initplot(genes):
"""
Starts a figure and initiates colors
:param genes:
:return: axis handle, colors for the genome values and colors for the lines
"""
cm_subsection = linspace(0, 1, len(genes[0]) + 2)
colors = [cm.summer(x) for x in cm_subsection]
colors2 = [cm.Reds(x) for x in cm_subsection]
fig = plt.figure(figsize=(10, 15))
ax = fig.add_subplot(111)
return ax, colors, colors2
def update_sensitivity_plot(fig, ax, sens, spec, title=''):
""" update a ROC plot """
mem = 10000
sens = sens[max(0, len(sens) - mem):]
spec = spec[max(0, len(spec) - mem):]
ax.clear()
ax.set_ylim((-0.05, 1.05))
ax.set_xlim((-0.05, 1.05))
ax.set_xlabel('1-specificity')
ax.set_ylabel('sensitivity')
ax.scatter(1 - np.array(spec),
sens,
c=cm.Reds(np.arange(0, 1.0, 1.0 / float(len(sens)))),
linewidths=0.2)
ax.plot([0, 1], [0, 1])
ax.set_title(title, size=16)
def calculate_on_target(ax, barcodes, expected, barcode_map=barcode_map):
"""Plots number of on target and off target barcodes as pie chart
ax : matplotlib axis
axis to plot on
barcodes : Counter
Counter object of barcode -> counts for each barcode counted
expected : list
list of barcodes (R01, R02..._ that are expected from this experiment
barcode_map : dict
dictionary barcode sequence -> human readable name
"""
total = 0
on_target = 0
off_target = 0
no_target = 0
expected_counts = []
off_target_counts = []
expected_names = []
off_target_names = []
for barcode, count in barcodes.items():
if barcode in barcode_map:
if count > 10000:
if barcode_map[barcode] in expected:
on_target += count
expected_counts.append(count)
expected_names.append(barcode_map[barcode])
else:
off_target += count
off_target_counts.append(count)
off_target_names.append(barcode_map[barcode])
else:
no_target += count
total += count
expected_colors = cm.Blues(np.linspace(0, 1, len(expected_counts)))
off_target_colors = cm.Reds(np.linspace(0, 1, len(off_target_counts) + 1))
patches, texts = ax.pie(
expected_counts + off_target_counts + [no_target],
labels=expected_names + off_target_names + ["No Barcode"],
colors=np.concatenate((expected_colors, off_target_colors)),
)
[text.set_fontsize(16) for text in texts]
def makeHeatMap(fname,wname,image,bins):
f = open(fname)
coords = np.array([[0,0]])
g = open(wname)
weights = []
for weight in g:
weight = weight.translate(None, '()[]')
weight = weight.split(',')[1]
weight = float(weight)
weights.append(weight)
i = 0
#print(weights)
for line in f:
#print(i)
line = line.translate(None, '[]')
point = line.split(',')
point = map(float, point)
point = map(abs,point)
#print(genCircle(point,100).shape)
coords = np.append(coords,genCircle(point,int(weights[i]*100000)),axis=0)
i = i+1
coords = coords[1:]
print(coords.shape)
bg = imread(image)
hmap, extent = heatmap(coords[:,0], coords[:,1], 1.5,bins)
print(hmap.shape)
#hmap = hmap[~np.all(hmap == 0, axis=1)]
#hmap = hmap[hmap!=[0.0,0.0]]
alphas = np.clip(Normalize(0, hmap.max(), clip=True)(hmap)*1.5, 0.0, 1.)
colors = Normalize(0, hmap.max(), clip=True)(hmap)
colors = cm.Reds(colors)
colors[..., -1] = alphas
fig, ax = plt.subplots(figsize=(24,24))
if "erangel" in image:
ax.set_xlim(0, 4096); ax.set_ylim(0, 4096)
else:
ax.set_xlim(0, 1000); ax.set_ylim(0, 1000)
ax.imshow(bg)
ax.imshow(colors, extent=extent, origin='lower', cmap=cm.Reds, alpha=1.0)
#plt.scatter(coords[:,0], coords[:,1])
plt.gca().invert_yaxis()
plt.savefig("../Plots/" + fname[11:-3]+"jpg")
def draw_convex_combination_3d(points, cc_points, sides=None, color_z=True):
fig = plt.figure()
# To create a 3D plot a sublot with projection='3d' must be created.
# For this to work required is the import of Axes3D: "from mpl_toolkits.mplot3d import Axes3D"
ax = fig.add_subplot(111, projection='3d')
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
# TODO: Zadanie 4.3: Zaimplementuj rysowanie wykresu 3D dla cc_points. Możesz dodatkowo zaimplementować kolorowanie względem wartości na osi z.
z_colours = [
cm.Reds((z + 1) / 2)
for z in (cc_points[:, 2] - np.min(cc_points[:, 2])) /
np.ptp(cc_points[:, 2])
]
ax.scatter(cc_points[:, 0], cc_points[:, 1], cc_points[:, 2], c=z_colours)
# Drawing contour of the figure (with plt.plot).
if sides is not None:
draw_contour_3d(points, sides)
def _viz_transition_t(scenario: ExperimentScenario, example: Dict, t: int):
action = index_batch_time(example, fwd_model.action_keys, b=t, t=0)
s0 = index_batch_time_with_metadata(metadata,
example,
fwd_model.state_keys,
b=t,
t=0)
s1 = index_batch_time_with_metadata(metadata,
example,
fwd_model.state_keys,
b=t,
t=1)
if 'accept_probablity' in example:
accept_probability_t = example['accept_probability'][t]
color = cm.Reds(accept_probability_t)
else:
color = "#aa2222aa"
scenario.plot_state_rviz(s0, label='', color='#ff0000ff')
scenario.plot_state_rviz(s1, label='predicted', color=color)
scenario.plot_action_rviz(s0, action, label='')
def __init__(self,data_pred,data_gt,colors,img,types,gif_name = "test.gif", plot_ = False, save = True):
self.img = img
self.xs_pred = data_pred[:,:,0]
self.ys_pred = data_pred[:,:,1]
self.xs_gt = data_gt[:,:,0]
self.ys_gt = data_gt[:,:,1]
self.types = types
self.nb_agents = self.xs_pred.shape[0]
self.margin = 1
self.nb_frames = self.xs_pred.shape[1]
self.gif_name = gif_name
self.plot_ = plot_
self.save = save
self.fps = 1
self.colors = colors
self.lin_size = 100
lin = np.linspace(0.6, 0.8, self.lin_size)
self.color_dict = {
"bicycle":cm.Blues(lin),
"pedestrian":cm.Reds(lin),
"car":cm.Greens(lin),
"skate":cm.Greys(lin),
"cart":cm.Purples(lin),
"bus":cm.Oranges(lin)
}
self.colors = [self.color_dict[type_][np.random.randint(self.lin_size)] for type_ in self.types]
self.history = 4
self.get_plots()
def get_transformer_config():
nodes = [8, 8]
fpaths, tags, legends, colors = [], [], [], []
fpath = 'results_dir/transformer_{tag}_test.out'
ps_tags = ['ps_sm', 'ps']
ps_legends = ['SGP (25K batch)', 'SGP (400K batch)']
ps_colors = [cm.Blues(x) for x in np.linspace(0.3, 0.8, len(ps_tags))]
fpaths.append(fpath)
tags.append(ps_tags)
legends.append(ps_legends)
colors.append(ps_colors)
fpath = 'results_dir/transformer_{tag}_test.out'
ar_tags = ['ar_sm', 'ar']
ar_legends = ['SGD (25K batch)', 'SGD (400K batch)']
ar_colors = [cm.Reds(x) for x in np.linspace(0.3, 0.8, len(ar_tags))]
fpaths.append(fpath)
tags.append(ar_tags)
legends.append(ar_legends)
colors.append(ar_colors)
return nodes, fpaths, tags, legends, colors
def log_predictions(
self, pred: np.ndarray, clusterings: Tuple[List[np.ndarray],
List[np.ndarray],
List[np.ndarray]]
) -> None:
type_count = pred.shape[-1]
new_size = self.preprocessed_screen.shape[:2]
final_pred_size = (new_size[0] * int(type_count**.5),
new_size[1] * (type_count // int(type_count**.5)))
final_pred = np.zeros((*final_pred_size, 3), dtype=np.uint8)
original_pred = np.uint8(cm.viridis(pred)[:, :, :, :3] * 255)
for type in range(type_count):
pred = original_pred[:, :, type, :]
if clusterings is not None or self.prediction_overlay_factor > 0:
prev_size = pred.shape[:2]
pred = Image.fromarray(pred)
pred = pred.resize((new_size[1], new_size[0]))
pred = Image.blend(pred,
Image.fromarray(self.preprocessed_screen),
self.prediction_overlay_factor)
pred = np.array(pred)
if clusterings is not None:
clustering = tuple(x[type] for x in clusterings)
cluster_colors = cm.Reds(
np.linspace(0, 1, len(clustering[2])))[:, :3] * 255
for cluster in zip(*clustering[:2]):
cl_ind = np.where(clustering[2] == cluster[1])[0]
if len(cl_ind) > 0:
y, x = tuple(cluster[0][:2] * new_size //
prev_size)
pred[y:y + self.cluster_color_size, x:x + self.cluster_color_size] \
= cluster_colors[cl_ind[0]]
type_x = type // (final_pred_size[1] // new_size[1])
type_y = type % (final_pred_size[1] // new_size[1])
final_pred[type_x * new_size[0]:(type_x + 1) * new_size[0],
type_y * new_size[1]:(type_y + 1) * new_size[1]] = pred
self.log_image('Predictions', final_pred)
def __init__(self, ax, mean, confint, std, values, clicklim=0.05):
self.fig = ax.figure
self.diff = []
self.values = values
self.ax = ax
self.mean = mean
self.confint = confint
self.std = std
self.ycoords = []
self.xcoords = []
self.clicklim = clicklim
self.horizontal_line1 = ax.axhline(y=0.4, color='black', alpha=0.5)
self.horizontal_line2 = ax.axhline(y=0.7, color='black', alpha=0.5)
self.hspan = ax.axhspan(2, 4, facecolor='gray', alpha=0.3)
self.text1 = ax.text(0, 0.4, "")
self.text2 = ax.text(0, 0.7, "")
self.ax.bar(self.values,
self.mean,
yerr=self.confint,
edgecolor='black',
color=cm.Reds(tuple(self.confint / 10000)))
self.fig.canvas.mpl_connect('button_press_event', self.onclick)
defocus_zernike[0, 1] = 1.0
defocus_actuators = zernike_fit.fit_zernike_wave_to_actuators(
defocus_zernike, plot=True, cmap='Reds')[:, 0]
# Loop over the strength of defocus to see what is the optimum value
rms_before, rms_after = [], []
diversities, rms_div = [], []
mean_peak_foc = []
# Noise RMS
N_cases = 30
noiseSNR = np.array([500, 250, 100])
N_noise = noiseSNR.shape[0]
rms_after_noisy = np.zeros((N_noise, N_cases))
rms_div_noisy = np.zeros((N_noise, N_cases))
colors = cm.Reds(np.linspace(0.5, 0.75, N_noise))
# beta = np.linspace(0.30, 4.0, N_cases)
beta = np.linspace(0.25, 7.0, N_cases)
N_foc = beta.shape[0]
# fig, axes = plt.subplots(N_foc, 3)
for k_noise in range(N_noise):
for i_beta, b in enumerate(beta):
print("\nBeta: %.2f" % b)
# Update the Diversity Map on the actuator model so that it matches Defocus
diversity_defocus = b * defocus_actuators / (2 * np.pi)
PSF_actuators.define_diversity(diversity_defocus)
# plt.figure()
# # diff_foc = p_foc_anam - p_foc
#
# fake_psf_foc, s = PSF_zernike.compute_PSF(x + x_coef + defocus_zernike)
# # fake_diff_foc = fake_psf_foc - p_foc
#
# foc_diff = (fake_psf_foc - p_foc_anam).flatten()
#
# total = np.concatenate([nom_diff, 0.1*foc_diff])
# print(total.shape)
return nom_diff
# ratios = [1.05, 1.10, 1.25]
ratios = [1.05]
markers = ['^', 'v', 'd', 'o']
colors = cm.Reds(np.linspace(0.5, 1.0, 3))
plt.figure()
for j, r in enumerate(ratios):
# (1) We define the anamorphic PSF model
anamorphic_ratio = r
zernike_matrices_anam = psf.zernike_matrix(N_levels=N_levels, rho_aper=RHO_APER, rho_obsc=RHO_OBSC, N_PIX=N_PIX,
radial_oversize=1.0, anamorphic_ratio=anamorphic_ratio)
zernike_matrix_anam, pupil_mask_zernike_anam, flat_zernike_anam = zernike_matrices_anam
zernike_matrices_anam = [zernike_matrix_anam, pupil_mask_zernike_anam, flat_zernike_anam]
PSF_zernike_anam = psf.PointSpreadFunction(matrices=zernike_matrices_anam, N_pix=N_PIX,
crop_pix=pix, diversity_coef=np.zeros(zernike_matrix.shape[-1]))
PSF_zernike_anam.define_diversity(defocus_zernike)
x0 = np.random.uniform(low=-0.1, high=0.1, size=N_zern)