def draw(options):
files = [f for f in os.listdir(options['outdir']) if f.endswith('.data')]
degrees = list()
diameters = list()
velocities = list()
for f in files:
fin = open(options['outdir']+'/'+f, 'r')
ts = -1
for line in fin:
if line.startswith('#'):
continue
time, degree, diameter, velocity = [t.strip() for t in line.split(',')]
time = int(time)
assert(ts == time-1)
ts = time
try:
degrees[time].append(float(degree))
diameters[time].append(int(diameter))
velocities[time].append(float(velocity))
except IndexError:
degrees.append([float(degree)])
diameters.append([int(diameter)])
velocities.append([float(velocity)])
polies = list()
times = range(len(degrees))
times2 = times + times[::-1]
degrees_conf_upper = [confidence(d)[0] for d in degrees]
degrees_conf_lower = [confidence(d)[1] for d in degrees]
polies.append(conf2poly(times, degrees_conf_upper, degrees_conf_lower, color='blue'))
diameters_conf_upper = [confidence(d)[0] for d in diameters]
diameters_conf_lower = [confidence(d)[1] for d in diameters]
polies.append(conf2poly(times, diameters_conf_upper, diameters_conf_lower, color='blue'))
velocities_conf_upper = [confidence(d)[0] for d in velocities]
velocities_conf_lower = [confidence(d)[1] for d in velocities]
polies.append(conf2poly(times, velocities_conf_upper, velocities_conf_lower, color='green'))
velocities = [scipy.mean(d) for d in velocities]
diameters = [scipy.mean(d) for d in diameters]
degrees = [scipy.mean(d) for d in degrees]
fig = MyFig(options, figsize=(10, 8), xlabel='Time [s]', ylabel='Metric', grid=False, legend=True, aspect='auto', legend_pos='upper right')
patch_collection = PatchCollection(polies, match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig.ax.add_collection(patch_collection)
fig.ax.plot(times, degrees, label='Mean degree', color='blue')
fig.ax.plot(times, diameters, label='Diameter', color='red')
fig.ax.plot(times, velocities, label='Mean velocity $[m/s]$', color='green')
fig.ax.set_xlim(0, options['duration'])
y_max = max(max(degrees), max(diameters), max(velocities))
fig.ax.set_ylim(0, y_max+10)
fig.save('metrics', fileformat='pdf')
def draw(self, ax, colour='k', alpha=1., linestyle='-', linewidth=1., markers=None, facecolor='none', dashes=(1, 1), zorder=0): """ Draw the polygon on ax """ # Add the last point ptstoplot = self.verts.tolist() ptstoplot.append(ptstoplot[0]) ptstoplot = np.array(ptstoplot) if facecolor == 'none': try: if linestyle == '--': ax.plot(ptstoplot[:, 0], ptstoplot[:, 1], c=colour, alpha=alpha, ls=linestyle, dashes=dashes, lw=linewidth, marker=markers, zorder=zorder) else: ax.plot(ptstoplot[:, 0], ptstoplot[:, 1], c=colour, alpha=alpha, ls=linestyle, lw=linewidth, marker=markers, zorder=zorder) except IndexError: pass else: patches = [] filled_pol = mp.Polygon(self.verts) patches.append(filled_pol) collection = PatchCollection(patches, facecolors=facecolor) ax.add_collection(collection) collection.set_alpha(alpha) collection.set_edgecolor(colour) collection.set_linewidth(linewidth) collection.set_linestyle(linestyle)
def data2fig(data, X, options, legend_title, xlabel, ylabel=r'Reachability~$\reachability$'):
if options['grayscale']:
colors = options['graycm'](pylab.linspace(0, 1, len(data.keys())))
else:
colors = options['color'](pylab.linspace(0, 1, len(data.keys())))
fig = MyFig(options, figsize=(10, 8), xlabel=r'Sources~$\sources$', ylabel=ylabel, grid=False, aspect='auto', legend=True)
for j, nhdp_ht in enumerate(sorted(data.keys())):
d = data[nhdp_ht]
try:
mean_y = [scipy.mean(d[n]) for n in X]
except KeyError:
logging.warning('key \"%s\" not found, continuing...', nhdp_ht)
continue
confs_y = [confidence(d[n])[2] for n in X]
poly = [conf2poly(X, list(numpy.array(mean_y)+numpy.array(confs_y)), list(numpy.array(mean_y)-numpy.array(confs_y)), color=colors[j])]
patch_collection = PatchCollection(poly, match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig.ax.add_collection(patch_collection)
fig.ax.plot(X, mean_y, label='$%d$' % nhdp_ht, color=colors[j])
fig.ax.set_xticks(X)
fig.ax.set_xticklabels(['$%s$' % i for i in X])
fig.ax.set_ylim(0,1)
fig.legend_title = legend_title
return fig
def add_circles(self, ax, centers, radis):
circles = []
for c, r in zip(centers, radis):
circles.append(patches.Circle(tuple(c), r))
patch_collection = PatchCollection(circles)
patch_collection.set_facecolor("none")
patch_collection.set_edgecolor("blue")
patch_collection.set_linewidth(1.5)
patch_collection.set_linestyle("dashed")
ax.add_collection(patch_collection)
print "added %d circles" % len(circles)
def plot_site(options):
options['prefix'] = 'site'
fig = MyFig(options, figsize=(10, 8), legend=True, grid=False, xlabel=r'Probability $p_s$', ylabel=r'Reachability~$\reachability$', aspect='auto')
fig_vs = MyFig(options, figsize=(10, 8), legend=True, grid=False, xlabel=r'Fraction of Forwarded Packets~$\forwarded$', ylabel=r'Reachability~$\reachability$', aspect='auto')
if options['grayscale']:
colors = options['graycm'](pylab.linspace(0, 1.0, 3))
else:
colors = fu_colormap()(pylab.linspace(0, 1.0, 3))
nodes = 105
axins = None
if options['inset_loc'] >= 0:
axins = zoomed_inset_axes(fig_vs.ax, options['inset_zoom'], loc=options['inset_loc'])
axins.set_xlim(options['inset_xlim'])
axins.set_ylim(options['inset_ylim'])
axins.set_xticklabels([])
axins.set_yticklabels([])
mark_inset(fig_vs.ax, axins, loc1=2, loc2=3, fc="none", ec="0.5")
for i, (name, label) in enumerate(names):
data = parse_site_only(options['datapath'][0], name)
rs = numpy.array([r for p, r, std, conf, n, fw, fw_std, fw_conf in data if r <= options['limit']])
fws = numpy.array([fw for p, r, std, conf, n, fw, fw_std, fw_conf in data if r <= options['limit']])/(nodes-1)
ps = numpy.array([p for p, r, std, conf, n, fw, fw_std, fw_conf in data]) #[0:len(rs)])
yerr = numpy.array([conf for p,r,std,conf, n, fw, fw_std, fw_conf in data]) #[0:len(rs)])
patch_collection = PatchCollection([conf2poly(ps, list(rs+yerr), list(rs-yerr), color=colors[i])], match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig.ax.add_collection(patch_collection)
fig.ax.plot(ps, rs, label=label, color=colors[i])
fig_vs.ax.plot(fws, rs, label=label, color=colors[i])
if axins:
axins.plot(fws, rs, color=colors[i])
fig.ax.set_ylim(0, options['limit'])
fig.legend_title = 'Graph'
fig.save('graphs')
fig_vs.legend_title = 'Graph'
fig_vs.ax.set_xlim(0,1)
fig_vs.ax.set_ylim(0,1)
fig_vs.save('vs_pb')
count = params[1]
vecs = params[2:]
x = vecs[::2]
y = np.array(vecs[1::2])
polygon = Polygon(np.array([x, y]).transpose(),
True,
color='gray')
patches_polygon.append(polygon)
pcc = PatchCollection(patches_circle, match_original=False)
pcp = PatchCollection(patches_polygon, match_original=False)
if args.collision_status:
pcc.set_color('#85878b')
pcp.set_color('#85878b')
pcc.set_alpha(0.3)
pcp.set_alpha(0.3)
pcc.set_linestyle('dashed')
pcp.set_linestyle('dashed')
pcc.set_edgecolor('#73cdc9')
pcp.set_edgecolor('#73cdc9')
pcc.set_linewidth(0.4)
pcp.set_linewidth(0.4)
pcc.set_joinstyle('round')
pcp.set_joinstyle('round')
else:
pcc.set_color('gray')
pcp.set_color('gray')
ax.add_collection(pcc)
ax.add_collection(pcp)
if args.safety_certificate:
xyrs = []
for line in open(args.safety_certificate, 'r').readlines():
def plot_bond_site(options):
options['prefix'] = 'bond_site'
epsilon = numpy.finfo(numpy.float).eps
bins = 11
if options['grayscale']:
colors = options['graycm'](pylab.linspace(0, 1.0, bins))
else:
colors = options['color'](pylab.linspace(0, 1.0, bins))
try:
data_files = [(open('%s/results' % (options['datapath'][0]), 'r'), '')]
except IOError:
dirList = os.listdir(options['datapath'][0])
files = [f for f in dirList if f.startswith('results')]
data_files = [(open('%s/%s' % (options['datapath'][0], f), 'r'), f.replace('results', '')) for f in files]
for (data_file, suffix) in data_files:
bond_site = False
max_cluster = False
merge = dict()
for line_num, line in enumerate(data_file):
if line_num < 100 and line.find('bond-site') >= 0:
bond_site = True
if line_num < 10 and line.find('maximum cluster size') >=0:
max_cluster = True
if line.startswith('#') or line.isspace():
continue
tokens = line.split(':')[1].split(',')
# ps, pb, reachability, std, conf, replications
if len(tokens) == 9:
ps, pb, r, std, conf, n, fw, fw_std, fw_conf = tokens
t = ((float(ps), float(pb), float(r), float(std), float(conf), int(n), float(fw), float(fw_std), float(fw_conf)))
else:
ps, pb, r, std, conf, n = tokens
t = ((float(ps), float(pb), float(r), float(std), float(conf), int(n), 0.0, 0.0, 0.0))
try:
merge[(float(tokens[0]), float(tokens[1]))].append(t)
except KeyError:
merge[(float(tokens[0]), float(tokens[1]))] = [t]
fig_contour = MyFig(options, figsize=(10, 8), xlabel=r'Probability $p_s$', ylabel=r'Probability $p_b$', aspect='auto')
fig_pcolor = MyFig(options, figsize=(10, 8), xlabel=r'Probability $p_s$', ylabel=r'Probability $p_b$', aspect='auto')
fig_vs_pb = None
fig_vs_ps = None
if bond_site:
if max_cluster:
ylabel= 'Max. Percolation Cluster Size'
else:
ylabel= 'Mean Percolation Cluster Size'
else:
fig_vs_pb = MyFig(options, figsize=(10, 8), legend=(not options['no_legend']), grid=False, xlabel=r'Fraction of Forwarded Packets~$\forwarded$', ylabel=r'Reachability~$\reachability$', aspect='auto')
fig_vs_ps = MyFig(options, figsize=(10, 8), legend=(not options['no_legend']), grid=False, xlabel=r'Fraction of Forwarded Packets~$\forwarded$', ylabel=r'Reachability~$\reachability$', aspect='auto')
fig_fw_pb = MyFig(options, figsize=(10, 8), legend=(not options['no_legend']), grid=False, xlabel=r'Probability $p_s$', ylabel=r'Fraction of Forwarded Packets~$\forwarded$', aspect='auto')
fig_fw_ps = MyFig(options, figsize=(10, 8), legend=(not options['no_legend']), grid=False, xlabel=r'Probability $p_b$', ylabel=r'Fraction of Forwarded Packets~$\forwarded$', aspect='auto')
ylabel = r'Reachability~$\reachability$'
fig_site = MyFig(options, figsize=(10, 8), legend=(not options['no_legend']), grid=False, xlabel=r'Probability $p_s$', ylabel=ylabel, aspect='auto')
fig_bond = MyFig(options, figsize=(10, 8), legend=(not options['no_legend']), grid=False, xlabel=r'Probability $p_b$', ylabel=ylabel, aspect='auto')
def fit_data(X, Y, options):
init_params = [1.0, 0.0, 0.0, 1.0]
hyperbolic2 = lambda (a,b,c,d), x: 1/(map(lambda _x: a*_x, x)+b) # f(x) = 1/(ax+b)
hyperbolic4 = lambda (a,b,c,d), x: d/(map(lambda _x: a*_x, x)+b)+c # f(x) = d/(ax+b)+c
exponential = lambda (a,b,c,d), x: scipy.e**(a*(x+b))+c # f(x) = e^(-a(x+b))+c
fitfunc = locals()[options['fit']]
errfunc = lambda (a,b,c,d), x, y: y-fitfunc((a,b,c,d), x)
return scipy.optimize.leastsq(errfunc, init_params, args=(X, Y)), fitfunc
def contour_plot(tuples):
X = pylab.linspace(0, 1, scipy.sqrt(len(tuples)))
Y = pylab.linspace(0, 1, scipy.sqrt(len(tuples)))
Z = numpy.array([r for p, pb, r in tuples]).reshape((len(X), len(Y))).transpose()
X, Y = pylab.meshgrid(X, Y)
if options['grayscale']:
pcolor = fig_contour.ax.contourf(X, Y, Z, levels=pylab.linspace(0, 1, 101), cmap=options['graycm'], antialiased=True, linestyles=None)
else:
pcolor = fig_contour.ax.contourf(X, Y, Z, levels=pylab.linspace(0, 1, 101), cmap=fu_colormap(), antialiased=True, linestyles=None)
cbar = fig_contour.colorbar(pcolor)
cbar.set_ticks(pylab.linspace(0, 1, 11))
if options['grayscale']:
pcolor = fig_pcolor.ax.pcolormesh(X, Y, Z, vmin=0, vmax=1, cmap=options['graycm'])
else:
pcolor = fig_pcolor.ax.pcolormesh(X, Y, Z, vmin=0, vmax=1, cmap=fu_colormap())
cbar = fig_pcolor.colorbar(pcolor)
cbar.set_ticks(pylab.linspace(0, 1, 11))
data = calc_metrics(merge)
tuples = [(ps, pb, r) for ps, pb, r, _std, _conf, _n, _fw_mean, _fw_std, _fw_std in data]
contour_plot(tuples)
nodes = options['nodes']
for i, bin in enumerate(pylab.linspace(0, 1, bins)):
r_pb1 = numpy.array([r for _ps, pb, r, _std, _conf, _n, _fw_mean, _fw_std, _fw_conf in data if abs(pb - bin) < epsilon*2])
fw_pb1 = numpy.array([fw_mean for _ps, pb, _r, _std, _conf, _n, fw_mean, _fw_std, _fw_conf in data if abs(pb - bin) < epsilon*2])/nodes
fw_conf_pb1 = numpy.array([fw_conf for _ps, pb, _r, _std, _conf, _n, fw_mean, _fw_std, fw_conf in data if abs(pb - bin) < epsilon*2])/nodes
conf_pb1 = numpy.array([conf for _ps, pb, _r, _std, conf, _n, _fw_mean, _fw_std, _fw_conf in data if abs(pb - bin) < epsilon*2])
p_pb1 = numpy.array([ps for ps, pb, _r, _std, _conf, _n, _fw_mean, _fw_std, _fw_conf in data if abs(pb - bin) < epsilon*2])
r_ps1 = numpy.array([r for ps, _pb, r, _std, _conf, n, _fw_mean, _fw_std, _fw_conf in data if abs(ps - bin) < epsilon*2])
fw_ps1 = numpy.array([fw_mean for ps, _pb, r, _std, _conf, n, fw_mean, _fw_std, _fw_conf in data if abs(ps - bin) < epsilon*2])/nodes
fw_conf_ps1 = numpy.array([fw_conf for ps, _pb, r, _std, _conf, n, fw_mean, _fw_std, fw_conf in data if abs(ps - bin) < epsilon*2])/nodes
conf_ps1 = numpy.array([conf for ps, _pb, _r, _std, conf, _n, _fw_mean, _fw_std, _fw_conf in data if abs(ps - bin) < epsilon*2])
p_ps1 = numpy.array([pb for ps, pb, _r, _std, _conf, n, _fw_mean, _fw_std, _fw_conf in data if abs(ps - bin) < epsilon*2])
assert(len(r_pb1) == len(conf_pb1) == len(p_pb1))
assert(len(r_ps1) == len(conf_ps1) == len(p_ps1))
if len(r_pb1) > 0:
if not options['noconfidence']:
patch_collection = PatchCollection([conf2poly(p_pb1, list(r_pb1+conf_pb1), list(r_pb1-conf_pb1), color=colors[i])], match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig_site.ax.add_collection(patch_collection)
fig_site.ax.plot(p_pb1, r_pb1, color=colors[i], label='$%.2f$' % bin)
if fig_vs_pb:
fig_vs_pb.ax.plot(fw_pb1, r_pb1, color=colors[i], label='$%.2f$' % bin)
patch_collection = PatchCollection([conf2poly(p_pb1, list(fw_pb1+fw_conf_pb1), list(fw_pb1-fw_conf_pb1), color=colors[i])], match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig_fw_pb.ax.add_collection(patch_collection)
fig_fw_pb.ax.plot(p_pb1, fw_pb1, color=colors[i], label='$%.2f$' % bin)
else:
fig_site.ax.plot(p_pb1, r_pb1, color=colors[i], label='$%.2f$' % bin)
if fig_vs_pb:
fig_vs_pb.ax.plot(fw_pb1, r_pb1, color=colors[i], label='$%.2f$' % bin)
fig_fw_pb.ax.plot(p_pb1, fw_pb1, color=colors[i], label='$%.2f$' % bin)
if len(r_ps1) > 0:
if not options['noconfidence']:
patch_collection = PatchCollection([conf2poly(p_ps1, list(r_ps1+conf_ps1), list(r_ps1-conf_ps1), color=colors[i])], match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig_bond.ax.add_collection(patch_collection)
fig_bond.ax.plot(p_ps1, r_ps1, color=colors[i], label='$%.2f$' % bin)
if fig_vs_ps:
fig_vs_ps.ax.plot(fw_ps1, r_ps1, color=colors[i], label='$%.2f$' % bin)
patch_collection = PatchCollection([conf2poly(p_ps1, list(fw_ps1+fw_conf_ps1), list(fw_ps1-fw_conf_ps1), color=colors[i])], match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig_fw_ps.ax.add_collection(patch_collection)
fig_fw_ps.ax.plot(p_ps1, fw_ps1, color=colors[i], label='$%.2f$' % bin)
else:
fig_bond.ax.plot(p_ps1, r_ps1, color=colors[i], label='$%.2f$' % bin)
if fig_vs_ps:
fig_vs_ps.ax.plot(fw_ps1, r_ps1, color=colors[i], label='$%.2f$' % bin)
fig_fw_ps.ax.plot(p_ps1, fw_ps1, color=colors[i], label='$%.2f$' % bin)
X = [p for p, pb, r in tuples if r < bin and r >= bin-0.1]
Y = [pb for ps, pb, r in tuples if r < bin and r >= bin-0.1]
assert(len(X) == len(Y))
if len(X) >= 4 and len(options['fit']):
(fitted_params, success), fitfunc = fit_data(X, Y, options)
#print fitted_params, success
min_x = min(X)
while fitfunc(fitted_params, [min_x]) <= 1.0 and min_x >= 0.0:
min_x -= 0.01
max_x = max(X)
while fitfunc(fitted_params, [max_x]) >= 0.0 and max_x <= 1.0:
max_x += 0.01
xfit = pylab.linspace(min_x, max_x, 100)
fig_contour.ax.plot(xfit, fitfunc(fitted_params, xfit), color='black', lw=2, label='%.2f' % bin)
for f in [fig_contour, fig_pcolor, fig_site, fig_bond]:
f.ax.set_xlim(0, 1)
f.ax.set_ylim(0, 1)
fig_site.legend_title = '$p_b$'
fig_bond.legend_title = '$p_s$'
fig_contour.save('contour%s' % suffix)
fig_pcolor.save('pcolor%s' % suffix)
fig_site.save('graph-site%s' % suffix)
fig_bond.save('graph-bond%s' % suffix)
if fig_vs_ps:
fig_vs_ps.ax.set_xlim(0,1)
fig_vs_ps.ax.set_ylim(0,1)
fig_vs_ps.legend_title = '$p_s$'
fig_vs_ps.save('vs_ps')
fig_fw_ps.ax.set_xlim(0,1)
fig_fw_ps.ax.set_ylim(0,1)
fig_fw_ps.legend_title = '$p_s$'
fig_fw_ps.save('fw_ps')
fig_vs_pb.ax.set_xlim(0,1)
fig_vs_pb.ax.set_ylim(0,1)
fig_vs_pb.legend_title = '$p_b$'
fig_vs_pb.save('vs_pb')
fig_fw_pb.ax.set_xlim(0,1)
fig_fw_pb.ax.set_ylim(0,1)
fig_fw_pb.legend_title = '$p_b$'
fig_fw_pb.save('fw_pb')
def show_annotated(imgid, anns_by_loss, gt, img_output_path):
#import pdb; pdb.set_trace(); 1
common_categories = set()
for loss, anns in anns_by_loss.iteritems():
#c = (np.random.random((1, 3))*0.6+0.4).tolist()[0]
gtcolor = [1.0, .25, .5]
#import pdb; pdb.set_trace(); 1
categories = [a['category_id'] for a in anns['dt'] if a['score'] > 0.8]
common_categories.update(categories)
common_categories = list(common_categories)
if len(common_categories) < 1:
return
for loss, anns in anns_by_loss.iteritems():
ax = plt.gca()
ax.set_autoscale_on(False)
dtcolor = COLORS[loss]
for category_id in common_categories:
gt_polygons = []
dt_polygons = []
color = []
gta = [a for a in anns['gt'] if a['category_id'] == category_id]
if len(gta) < 1:
continue
gtbbox = gta[0]['bbox']
#x,y,w,h
gtpoly = Rectangle((gtbbox[0], gtbbox[1]), gtbbox[2], gtbbox[3])
gt_polygons.append(gtpoly)
color.append(COLORS['white'])
dt = [a for a in anns['dt'] if a['category_id'] == category_id]
if len(dt) < 1:
continue
dt = sorted(dt, key=lambda a: a['score'])
dtbbox = dt[0]['bbox']
#x,y,w,h
dtpoly = Rectangle((dtbbox[0], dtbbox[1]), dtbbox[2], dtbbox[3])
dt_polygons.append(dtpoly)
color.append(COLORS['white'])
# top, left, bottom, right
gtbb = gtbbox[1], gtbbox[
0], gtbbox[1] + gtbbox[3], gtbbox[0] + gtbbox[2]
dtbb = dtbbox[1], dtbbox[
0], dtbbox[1] + dtbbox[3], dtbbox[0] + dtbbox[2]
iou = iou_utils.iou(gtbb, dtbb)
giou = iou_utils.giou(gtbb, dtbb)
txt = ax.text(0.5,
0.1,
"IoU: %.3f, GIoU: %.3f" % (iou, giou),
horizontalalignment='center',
verticalalignment='center',
transform=ax.transAxes,
color=COLORS['white'],
family='serif',
size=26)
txt.set_path_effects(
[PathEffects.withStroke(linewidth=4, foreground='black')])
#p = PatchCollection(polygons, facecolor=color, linewidths=0, alpha=0.4)
#ax.add_collection(p)
# gt
p = PatchCollection(gt_polygons,
facecolor='none',
edgecolors=color,
linewidths=4)
p.set_linestyle('solid')
ax.add_collection(p)
# dt
p = PatchCollection(dt_polygons,
facecolor='none',
edgecolors=color,
linewidths=4)
p.set_linestyle('dashed')
ax.add_collection(p)
#1 category only
break
#import pdb; pdb.set_trace(); 1
imgfname = gt.imgs[imgid]['file_name']
_, split, _ = imgfname.split('_')
src_img = "{}/coco/coco/images/{}/{}".format(DATASETS, split, imgfname)
img = mpimg.imread(src_img)
#ax.add_image(img)
#ax.figure.figimage(img)
ax.autoscale()
ax.imshow(img)
ax.axes.get_xaxis().set_visible(False)
ax.axes.get_yaxis().set_visible(False)
ax.set_frame_on(False)
#import pdb; pdb.set_trace(); 1
imgpath = "{}/{}_category-{}-{}.jpg".format(img_output_path, imgid,
common_categories[0], loss)
print("imgpath: {}".format(imgpath))
ax.figure.savefig(imgpath, dpi=400, bbox_inches='tight', pad_inches=0)
plt.clf()
def draw(options):
files = [f for f in os.listdir(options['outdir']) if f.endswith('.data')]
degrees = list()
diameters = list()
velocities = list()
for f in files:
fin = open(options['outdir'] + '/' + f, 'r')
ts = -1
for line in fin:
if line.startswith('#'):
continue
time, degree, diameter, velocity = [
t.strip() for t in line.split(',')
]
time = int(time)
assert (ts == time - 1)
ts = time
try:
degrees[time].append(float(degree))
diameters[time].append(int(diameter))
velocities[time].append(float(velocity))
except IndexError:
degrees.append([float(degree)])
diameters.append([int(diameter)])
velocities.append([float(velocity)])
polies = list()
times = range(len(degrees))
times2 = times + times[::-1]
degrees_conf_upper = [confidence(d)[0] for d in degrees]
degrees_conf_lower = [confidence(d)[1] for d in degrees]
polies.append(
conf2poly(times, degrees_conf_upper, degrees_conf_lower, color='blue'))
diameters_conf_upper = [confidence(d)[0] for d in diameters]
diameters_conf_lower = [confidence(d)[1] for d in diameters]
polies.append(
conf2poly(times,
diameters_conf_upper,
diameters_conf_lower,
color='blue'))
velocities_conf_upper = [confidence(d)[0] for d in velocities]
velocities_conf_lower = [confidence(d)[1] for d in velocities]
polies.append(
conf2poly(times,
velocities_conf_upper,
velocities_conf_lower,
color='green'))
velocities = [scipy.mean(d) for d in velocities]
diameters = [scipy.mean(d) for d in diameters]
degrees = [scipy.mean(d) for d in degrees]
fig = MyFig(options,
figsize=(10, 8),
xlabel='Time [s]',
ylabel='Metric',
grid=False,
legend=True,
aspect='auto',
legend_pos='upper right')
patch_collection = PatchCollection(polies, match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig.ax.add_collection(patch_collection)
fig.ax.plot(times, degrees, label='Mean degree', color='blue')
fig.ax.plot(times, diameters, label='Diameter', color='red')
fig.ax.plot(times,
velocities,
label='Mean velocity $[m/s]$',
color='green')
fig.ax.set_xlim(0, options['duration'])
y_max = max(max(degrees), max(diameters), max(velocities))
fig.ax.set_ylim(0, y_max + 10)
fig.save('metrics', fileformat='pdf')
def show_annotated(imgid,
anns_by_loss,
gt,
img_output_path,
txt_output_path,
network='yolo'):
global colormod
#import pdb; pdb.set_trace(); 1
common_categories = set()
for loss, anns in anns_by_loss.iteritems():
#c = (np.random.random((1, 3))*0.6+0.4).tolist()[0]
gtcolor = [1.0, .25, .5]
#import pdb; pdb.set_trace(); 1
categories = [a['category_id'] for a in anns['dt']]
common_categories.update(categories)
common_categories = list(common_categories)
if len(common_categories) < 1:
return
avggious = dict(mse=False, iou=False, giou=False)
avgious = dict(mse=False, iou=False, giou=False)
biggestboxscores = {}
for loss, anns in anns_by_loss.iteritems():
avggious[loss] = []
avgious[loss] = []
ax = plt.gca()
ax.set_autoscale_on(False)
gcolor = []
dcolor = []
dtcolor = COLORS[loss]
bbox_txt = []
#for cidx, category_id in enumerate(common_categories):
gt_polygons = []
dt_polygons = []
#gta = [a for a in anns['gt'] if a['category_id'] == category_id]
gta = anns['gt']
if len(gta) < 1:
continue
gtbboxes = [b['bbox'] for b in gta]
#dt = [a for a in anns['dt'] if a['category_id'] == category_id]
dt = anns['dt']
dtbboxes = [b['bbox'] for b in dt]
# gious shape(dt, gt)
gious = np.zeros((len(gtbboxes), len(dtbboxes)))
for i, g in enumerate(gtbboxes):
for j, d in enumerate(dtbboxes):
# top, left, bottom, right
gtbb = g[1], g[0], g[1] + g[3], g[0] + g[2]
dtbb = d[1], d[0], d[1] + d[3], d[0] + d[2]
gious[i, j] = iou_utils.giou(gtbb, dtbb)
#sortby = np.diagonal(gious)
#gtbboxes_s = [x for _, x in sorted(zip(sortby,gtbboxes), key=lambda pair: pair[0])]
#dtbboxes_s = [x for _, x in sorted(zip(sortby,dtbboxes), key=lambda pair: pair[0])]
for i, gtbbox in enumerate(gtbboxes):
gann = anns['gt'][i]
category_id = gann['category_id']
print("category_id: {}".format(category_id))
# find gt
dann = anns['dt'][np.argmax(gious[i])]
dtbbox = dtbboxes[np.argmax(gious[i])]
#x,y,w,h
#colormod += 1
c = color_names[category_id % len(color_names)]
det_c = c
# white detection bb if score < threshold
#det_c = c if dann['score'] >= SCORE_THRESHOLD else 'white'
gcolor.append(c)
dcolor.append(det_c)
gtbb = gtbbox[1], gtbbox[
0], gtbbox[1] + gtbbox[3], gtbbox[0] + gtbbox[2]
gtbbsize = (gtbb[2] - gtbb[0]) * (gtbb[3] - gtbb[1])
dtbb = dtbbox[1], dtbbox[
0], dtbbox[1] + dtbbox[3], dtbbox[0] + dtbbox[2]
giou = iou_utils.giou(gtbb, dtbb)
iou = iou_utils.iou(gtbb, dtbb)
avggious[loss].append(giou)
avgious[loss].append(iou)
#if gious.shape[0] > 1:
# import pdb; pdb.set_trace(); 1
bbox_txt.append(
"BB: {}, category_id: {}, color: {}, giou: {}, iou: {}".format(
i, category_id, c, giou, iou))
#iou = iou_utils.iou(gtbb, dtbb)
linewidth = 5
category_name = [
cat['name'] for cat in gt.dataset['categories']
if cat['id'] == category_id
][0]
score = dann['score']
if loss not in biggestboxscores:
biggestboxscores[loss] = None
if biggestboxscores[loss] is None or biggestboxscores[loss][
'box'] < gtbbsize:
biggestboxscores[loss] = {
'box': gtbbsize,
'score': score,
'category': category_name,
'metric': giou
}
print("TEXT COORDINATES: ({}, {}), class: {}, score: {}".format(
gtbbox[0], dtbbox[1], category_name, score))
#ax.text(dtbbox[0], dtbbox[1], category_name, horizontalalignment='left', verticalalignment='bottom', color=c, family='serif', size=10)
#if dann['score'] <= SCORE_THRESHOLD:
# ax.text(dtbbox[2], dtbbox[1], dann['score'], horizontalalignment='left', verticalalignment='bottom', color='white', family='serif', size=10)
gtpoly = Rectangle((gtbbox[0], gtbbox[1]), gtbbox[2], gtbbox[3])
gt_polygons.append(gtpoly)
p = PatchCollection(gt_polygons,
facecolor='none',
edgecolors='white',
linewidths=linewidth,
alpha=0.5,
zorder=i)
p.set_linestyle('solid')
ax.add_collection(p)
dtpoly = Rectangle((dtbbox[0], dtbbox[1]), dtbbox[2], dtbbox[3])
dt_polygons.append(dtpoly)
p = PatchCollection(dt_polygons,
facecolor='none',
edgecolors=dcolor,
linewidths=linewidth,
alpha=score,
zorder=len(gtbboxes) + i)
p.set_linestyle('dashed')
ax.add_collection(p)
#p = PatchCollection(dt_polygons, facecolor='none', edgecolors=dcolor, linewidths=linewidth, alpha=score)
#p.set_linestyle('dashed')
#ax.add_collection(p)
#txt = ax.text(0.5, 0.1, "IoU: %.3f, GIoU: %.3f" % (iou, giou), horizontalalignment='center', verticalalignment='center', transform=ax.transAxes, color=COLORS['white'], family='serif', size=26)
#txt.set_path_effects([PathEffects.withStroke(linewidth=4, foreground='black')])
#p = PatchCollection(polygons, facecolor=color, linewidths=0, alpha=0.4)
#ax.add_collection(p)
# gt
# dt
#1 category only
#if cidx >= PLOT_MAX_CATEGORIES:
# break
if avggious['giou'] != False:
#import pdb; pdb.set_trace(); 1
imgfname = gt.imgs[imgid]['file_name']
_, split, _ = imgfname.split('_')
src_img = "{}/coco/coco/images/{}/{}".format(
DATASETS, split, imgfname)
img = mpimg.imread(src_img)
#ax.add_image(img)
#ax.figure.figimage(img)
ax.autoscale()
ax.imshow(img)
ax.axes.get_xaxis().set_visible(False)
ax.axes.get_yaxis().set_visible(False)
ax.set_frame_on(False)
# range 0 <-> 2
mmse = 1 + np.mean(avggious['mse'])
mgiou = 1 + np.mean(avggious['giou'])
miou = 1 + np.mean(avggious['iou'])
scorestr = "%s%s%s" % (str(int(
mmse * 100)).zfill(3), str(int(
miou * 100)).zfill(3), str(int(mgiou * 100)).zfill(3))
basename = "{}-id_{}-mse_{}-iou_{}-giou_{}-category-{}-{}-{}".format(
scorestr, imgid, mmse, miou, mgiou, common_categories[0],
network, loss)
imgpath = "{}/{}.jpg".format(img_output_path, basename)
txtpath = "{}/{}.txt".format(txt_output_path, basename)
bbox_txt.insert(
0,
"AVG: giou metric: (giou loss: {}, iou loss: {}, mse loss: {}), iou metric: (giou loss: {}, iou loss: {}, mse loss: {})"
.format(np.mean(avggious['giou']), np.mean(avggious['iou']),
np.mean(avggious['mse']), np.mean(avgious['giou']),
np.mean(avgious['iou']), np.mean(avgious['mse'])))
with open(txtpath, 'wb') as f:
f.write('\n'.join(bbox_txt))
print("imgpath: {}".format(imgpath))
ax.figure.savefig(imgpath,
dpi=100,
bbox_inches='tight',
pad_inches=0)
plt.clf()
if 'giou' in biggestboxscores and 'iou' in biggestboxscores and 'mse' in biggestboxscores:
with open(os.path.join(txt_output_path, "scores.csv"), 'ab') as f:
f.write("{},{},{},{},{},{},{},{},{},{}\n".format(
imgid, biggestboxscores['giou']['score'],
biggestboxscores['iou']['score'],
biggestboxscores['mse']['score'],
biggestboxscores['giou']['category'],
biggestboxscores['iou']['category'],
biggestboxscores['mse']['category'],
biggestboxscores['giou']['metric'],
biggestboxscores['iou']['metric'],
biggestboxscores['mse']['metric']))
def plot_site(options):
options['prefix'] = 'site'
fig = MyFig(options,
figsize=(10, 8),
legend=True,
grid=False,
xlabel=r'Probability $p_s$',
ylabel=r'Reachability~$\reachability$',
aspect='auto')
fig_vs = MyFig(options,
figsize=(10, 8),
legend=True,
grid=False,
xlabel=r'Fraction of Forwarded Packets~$\forwarded$',
ylabel=r'Reachability~$\reachability$',
aspect='auto')
if options['grayscale']:
colors = options['graycm'](pylab.linspace(0, 1.0, 3))
else:
colors = fu_colormap()(pylab.linspace(0, 1.0, 3))
nodes = 105
axins = None
if options['inset_loc'] >= 0:
axins = zoomed_inset_axes(fig_vs.ax,
options['inset_zoom'],
loc=options['inset_loc'])
axins.set_xlim(options['inset_xlim'])
axins.set_ylim(options['inset_ylim'])
axins.set_xticklabels([])
axins.set_yticklabels([])
mark_inset(fig_vs.ax, axins, loc1=2, loc2=3, fc="none", ec="0.5")
for i, (name, label) in enumerate(names):
data = parse_site_only(options['datapath'][0], name)
rs = numpy.array([
r for p, r, std, conf, n, fw, fw_std, fw_conf in data
if r <= options['limit']
])
fws = numpy.array([
fw for p, r, std, conf, n, fw, fw_std, fw_conf in data
if r <= options['limit']
]) / (nodes - 1)
ps = numpy.array([
p for p, r, std, conf, n, fw, fw_std, fw_conf in data
]) #[0:len(rs)])
yerr = numpy.array([
conf for p, r, std, conf, n, fw, fw_std, fw_conf in data
]) #[0:len(rs)])
patch_collection = PatchCollection(
[conf2poly(ps, list(rs + yerr), list(rs - yerr), color=colors[i])],
match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig.ax.add_collection(patch_collection)
fig.ax.plot(ps, rs, label=label, color=colors[i])
fig_vs.ax.plot(fws, rs, label=label, color=colors[i])
if axins:
axins.plot(fws, rs, color=colors[i])
fig.ax.set_ylim(0, options['limit'])
fig.legend_title = 'Graph'
fig.save('graphs')
fig_vs.legend_title = 'Graph'
fig_vs.ax.set_xlim(0, 1)
fig_vs.ax.set_ylim(0, 1)
fig_vs.save('vs_pb')
def plot_bond_site(options):
options['prefix'] = 'bond_site'
epsilon = numpy.finfo(numpy.float).eps
bins = 11
if options['grayscale']:
colors = options['graycm'](pylab.linspace(0, 1.0, bins))
else:
colors = options['color'](pylab.linspace(0, 1.0, bins))
try:
data_files = [(open('%s/results' % (options['datapath'][0]), 'r'), '')]
except IOError:
dirList = os.listdir(options['datapath'][0])
files = [f for f in dirList if f.startswith('results')]
data_files = [(open('%s/%s' % (options['datapath'][0], f),
'r'), f.replace('results', '')) for f in files]
for (data_file, suffix) in data_files:
bond_site = False
max_cluster = False
merge = dict()
for line_num, line in enumerate(data_file):
if line_num < 100 and line.find('bond-site') >= 0:
bond_site = True
if line_num < 10 and line.find('maximum cluster size') >= 0:
max_cluster = True
if line.startswith('#') or line.isspace():
continue
tokens = line.split(':')[1].split(',')
# ps, pb, reachability, std, conf, replications
if len(tokens) == 9:
ps, pb, r, std, conf, n, fw, fw_std, fw_conf = tokens
t = ((float(ps), float(pb), float(r), float(std), float(conf),
int(n), float(fw), float(fw_std), float(fw_conf)))
else:
ps, pb, r, std, conf, n = tokens
t = ((float(ps), float(pb), float(r), float(std), float(conf),
int(n), 0.0, 0.0, 0.0))
try:
merge[(float(tokens[0]), float(tokens[1]))].append(t)
except KeyError:
merge[(float(tokens[0]), float(tokens[1]))] = [t]
fig_contour = MyFig(options,
figsize=(10, 8),
xlabel=r'Probability $p_s$',
ylabel=r'Probability $p_b$',
aspect='auto')
fig_pcolor = MyFig(options,
figsize=(10, 8),
xlabel=r'Probability $p_s$',
ylabel=r'Probability $p_b$',
aspect='auto')
fig_vs_pb = None
fig_vs_ps = None
if bond_site:
if max_cluster:
ylabel = 'Max. Percolation Cluster Size'
else:
ylabel = 'Mean Percolation Cluster Size'
else:
fig_vs_pb = MyFig(
options,
figsize=(10, 8),
legend=(not options['no_legend']),
grid=False,
xlabel=r'Fraction of Forwarded Packets~$\forwarded$',
ylabel=r'Reachability~$\reachability$',
aspect='auto')
fig_vs_ps = MyFig(
options,
figsize=(10, 8),
legend=(not options['no_legend']),
grid=False,
xlabel=r'Fraction of Forwarded Packets~$\forwarded$',
ylabel=r'Reachability~$\reachability$',
aspect='auto')
fig_fw_pb = MyFig(
options,
figsize=(10, 8),
legend=(not options['no_legend']),
grid=False,
xlabel=r'Probability $p_s$',
ylabel=r'Fraction of Forwarded Packets~$\forwarded$',
aspect='auto')
fig_fw_ps = MyFig(
options,
figsize=(10, 8),
legend=(not options['no_legend']),
grid=False,
xlabel=r'Probability $p_b$',
ylabel=r'Fraction of Forwarded Packets~$\forwarded$',
aspect='auto')
ylabel = r'Reachability~$\reachability$'
fig_site = MyFig(options,
figsize=(10, 8),
legend=(not options['no_legend']),
grid=False,
xlabel=r'Probability $p_s$',
ylabel=ylabel,
aspect='auto')
fig_bond = MyFig(options,
figsize=(10, 8),
legend=(not options['no_legend']),
grid=False,
xlabel=r'Probability $p_b$',
ylabel=ylabel,
aspect='auto')
def fit_data(X, Y, options):
init_params = [1.0, 0.0, 0.0, 1.0]
hyperbolic2 = lambda (a, b, c, d), x: 1 / (map(
lambda _x: a * _x, x) + b) # f(x) = 1/(ax+b)
hyperbolic4 = lambda (a, b, c, d), x: d / (map(
lambda _x: a * _x, x) + b) + c # f(x) = d/(ax+b)+c
exponential = lambda (a, b, c, d), x: scipy.e**(a * (
x + b)) + c # f(x) = e^(-a(x+b))+c
fitfunc = locals()[options['fit']]
errfunc = lambda (a, b, c, d), x, y: y - fitfunc((a, b, c, d), x)
return scipy.optimize.leastsq(errfunc, init_params,
args=(X, Y)), fitfunc
def contour_plot(tuples):
X = pylab.linspace(0, 1, scipy.sqrt(len(tuples)))
Y = pylab.linspace(0, 1, scipy.sqrt(len(tuples)))
Z = numpy.array([r for p, pb, r in tuples]).reshape(
(len(X), len(Y))).transpose()
X, Y = pylab.meshgrid(X, Y)
if options['grayscale']:
pcolor = fig_contour.ax.contourf(X,
Y,
Z,
levels=pylab.linspace(
0, 1, 101),
cmap=options['graycm'],
antialiased=True,
linestyles=None)
else:
pcolor = fig_contour.ax.contourf(X,
Y,
Z,
levels=pylab.linspace(
0, 1, 101),
cmap=fu_colormap(),
antialiased=True,
linestyles=None)
cbar = fig_contour.colorbar(pcolor)
cbar.set_ticks(pylab.linspace(0, 1, 11))
if options['grayscale']:
pcolor = fig_pcolor.ax.pcolormesh(X,
Y,
Z,
vmin=0,
vmax=1,
cmap=options['graycm'])
else:
pcolor = fig_pcolor.ax.pcolormesh(X,
Y,
Z,
vmin=0,
vmax=1,
cmap=fu_colormap())
cbar = fig_pcolor.colorbar(pcolor)
cbar.set_ticks(pylab.linspace(0, 1, 11))
data = calc_metrics(merge)
tuples = [
(ps, pb, r)
for ps, pb, r, _std, _conf, _n, _fw_mean, _fw_std, _fw_std in data
]
contour_plot(tuples)
nodes = options['nodes']
for i, bin in enumerate(pylab.linspace(0, 1, bins)):
r_pb1 = numpy.array([
r for _ps, pb, r, _std, _conf, _n, _fw_mean, _fw_std, _fw_conf
in data if abs(pb - bin) < epsilon * 2
])
fw_pb1 = numpy.array([
fw_mean for _ps, pb, _r, _std, _conf, _n, fw_mean, _fw_std,
_fw_conf in data if abs(pb - bin) < epsilon * 2
]) / nodes
fw_conf_pb1 = numpy.array([
fw_conf for _ps, pb, _r, _std, _conf, _n, fw_mean, _fw_std,
fw_conf in data if abs(pb - bin) < epsilon * 2
]) / nodes
conf_pb1 = numpy.array([
conf for _ps, pb, _r, _std, conf, _n, _fw_mean, _fw_std,
_fw_conf in data if abs(pb - bin) < epsilon * 2
])
p_pb1 = numpy.array([
ps for ps, pb, _r, _std, _conf, _n, _fw_mean, _fw_std, _fw_conf
in data if abs(pb - bin) < epsilon * 2
])
r_ps1 = numpy.array([
r for ps, _pb, r, _std, _conf, n, _fw_mean, _fw_std, _fw_conf
in data if abs(ps - bin) < epsilon * 2
])
fw_ps1 = numpy.array([
fw_mean for ps, _pb, r, _std, _conf, n, fw_mean, _fw_std,
_fw_conf in data if abs(ps - bin) < epsilon * 2
]) / nodes
fw_conf_ps1 = numpy.array([
fw_conf for ps, _pb, r, _std, _conf, n, fw_mean, _fw_std,
fw_conf in data if abs(ps - bin) < epsilon * 2
]) / nodes
conf_ps1 = numpy.array([
conf for ps, _pb, _r, _std, conf, _n, _fw_mean, _fw_std,
_fw_conf in data if abs(ps - bin) < epsilon * 2
])
p_ps1 = numpy.array([
pb for ps, pb, _r, _std, _conf, n, _fw_mean, _fw_std, _fw_conf
in data if abs(ps - bin) < epsilon * 2
])
assert (len(r_pb1) == len(conf_pb1) == len(p_pb1))
assert (len(r_ps1) == len(conf_ps1) == len(p_ps1))
if len(r_pb1) > 0:
if not options['noconfidence']:
patch_collection = PatchCollection([
conf2poly(p_pb1,
list(r_pb1 + conf_pb1),
list(r_pb1 - conf_pb1),
color=colors[i])
],
match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig_site.ax.add_collection(patch_collection)
fig_site.ax.plot(p_pb1,
r_pb1,
color=colors[i],
label='$%.2f$' % bin)
if fig_vs_pb:
fig_vs_pb.ax.plot(fw_pb1,
r_pb1,
color=colors[i],
label='$%.2f$' % bin)
patch_collection = PatchCollection([
conf2poly(p_pb1,
list(fw_pb1 + fw_conf_pb1),
list(fw_pb1 - fw_conf_pb1),
color=colors[i])
],
match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig_fw_pb.ax.add_collection(patch_collection)
fig_fw_pb.ax.plot(p_pb1,
fw_pb1,
color=colors[i],
label='$%.2f$' % bin)
else:
fig_site.ax.plot(p_pb1,
r_pb1,
color=colors[i],
label='$%.2f$' % bin)
if fig_vs_pb:
fig_vs_pb.ax.plot(fw_pb1,
r_pb1,
color=colors[i],
label='$%.2f$' % bin)
fig_fw_pb.ax.plot(p_pb1,
fw_pb1,
color=colors[i],
label='$%.2f$' % bin)
if len(r_ps1) > 0:
if not options['noconfidence']:
patch_collection = PatchCollection([
conf2poly(p_ps1,
list(r_ps1 + conf_ps1),
list(r_ps1 - conf_ps1),
color=colors[i])
],
match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig_bond.ax.add_collection(patch_collection)
fig_bond.ax.plot(p_ps1,
r_ps1,
color=colors[i],
label='$%.2f$' % bin)
if fig_vs_ps:
fig_vs_ps.ax.plot(fw_ps1,
r_ps1,
color=colors[i],
label='$%.2f$' % bin)
patch_collection = PatchCollection([
conf2poly(p_ps1,
list(fw_ps1 + fw_conf_ps1),
list(fw_ps1 - fw_conf_ps1),
color=colors[i])
],
match_original=True)
patch_collection.set_alpha(0.3)
patch_collection.set_linestyle('dashed')
fig_fw_ps.ax.add_collection(patch_collection)
fig_fw_ps.ax.plot(p_ps1,
fw_ps1,
color=colors[i],
label='$%.2f$' % bin)
else:
fig_bond.ax.plot(p_ps1,
r_ps1,
color=colors[i],
label='$%.2f$' % bin)
if fig_vs_ps:
fig_vs_ps.ax.plot(fw_ps1,
r_ps1,
color=colors[i],
label='$%.2f$' % bin)
fig_fw_ps.ax.plot(p_ps1,
fw_ps1,
color=colors[i],
label='$%.2f$' % bin)
X = [p for p, pb, r in tuples if r < bin and r >= bin - 0.1]
Y = [pb for ps, pb, r in tuples if r < bin and r >= bin - 0.1]
assert (len(X) == len(Y))
if len(X) >= 4 and len(options['fit']):
(fitted_params, success), fitfunc = fit_data(X, Y, options)
#print fitted_params, success
min_x = min(X)
while fitfunc(fitted_params, [min_x]) <= 1.0 and min_x >= 0.0:
min_x -= 0.01
max_x = max(X)
while fitfunc(fitted_params, [max_x]) >= 0.0 and max_x <= 1.0:
max_x += 0.01
xfit = pylab.linspace(min_x, max_x, 100)
fig_contour.ax.plot(xfit,
fitfunc(fitted_params, xfit),
color='black',
lw=2,
label='%.2f' % bin)
for f in [fig_contour, fig_pcolor, fig_site, fig_bond]:
f.ax.set_xlim(0, 1)
f.ax.set_ylim(0, 1)
fig_site.legend_title = '$p_b$'
fig_bond.legend_title = '$p_s$'
fig_contour.save('contour%s' % suffix)
fig_pcolor.save('pcolor%s' % suffix)
fig_site.save('graph-site%s' % suffix)
fig_bond.save('graph-bond%s' % suffix)
if fig_vs_ps:
fig_vs_ps.ax.set_xlim(0, 1)
fig_vs_ps.ax.set_ylim(0, 1)
fig_vs_ps.legend_title = '$p_s$'
fig_vs_ps.save('vs_ps')
fig_fw_ps.ax.set_xlim(0, 1)
fig_fw_ps.ax.set_ylim(0, 1)
fig_fw_ps.legend_title = '$p_s$'
fig_fw_ps.save('fw_ps')
fig_vs_pb.ax.set_xlim(0, 1)
fig_vs_pb.ax.set_ylim(0, 1)
fig_vs_pb.legend_title = '$p_b$'
fig_vs_pb.save('vs_pb')
fig_fw_pb.ax.set_xlim(0, 1)
fig_fw_pb.ax.set_ylim(0, 1)
fig_fw_pb.legend_title = '$p_b$'
fig_fw_pb.save('fw_pb')
def Plot2D(self, xy=None, elecon=None, u=None, color=None, ax=None, show=0,
weight=None, colorby=None, linestyle='-', label=None, xlim=None,
ylim=None, filename=None, **kwds):
assert self.dimensions == 2
from matplotlib.patches import Polygon
import matplotlib.lines as mlines
from matplotlib.collections import PatchCollection
from matplotlib.cm import coolwarm, Spectral
import matplotlib.pyplot as plt
if xy is None:
xy = array(self.coord)
if elecon is None:
elecon = []
for blk in self.eleblx:
elecon.extend(blk.elecon.tolist())
elecon = asarray(elecon)
if u is not None:
xy += u.reshape(xy.shape)
patches = []
for points in xy[elecon[:]]:
quad = Polygon(points, True)
patches.append(quad)
if ax is None:
fig, ax = plt.subplots()
#colors = 100 * random.rand(len(patches))
p = PatchCollection(patches, linewidth=weight, **kwds)
if colorby is not None:
colorby = asarray(colorby).flatten()
if len(colorby) == len(xy):
# average value in element
colorby = array([average(colorby[points]) for points in elecon])
p.set_cmap(Spectral) #coolwarm)
p.set_array(colorby)
p.set_clim(vmin=colorby.min(), vmax=colorby.max())
fig.colorbar(p)
else:
p.set_edgecolor(color)
p.set_facecolor('None')
p.set_linewidth(weight)
p.set_linestyle(linestyle)
if label:
ax.plot([], [], color=color, linestyle=linestyle, label=label)
ax.add_collection(p)
if not ylim:
ymin, ymax = amin(xy[:,1]), amax(xy[:,1])
dy = max(abs(ymin*.05), abs(ymax*.05))
ax.set_ylim([ymin-dy, ymax+dy])
else:
ax.set_ylim(ylim)
if not xlim:
xmin, xmax = amin(xy[:,0]), amax(xy[:,0])
dx = max(abs(xmin*.05), abs(xmax*.05))
ax.set_xlim([xmin-dx, xmax+dx])
else:
ax.set_xlim(xlim)
ax.set_aspect('equal')
if show:
plt.show()
if filename is not None:
plt.legend()
plt.savefig(filename, transparent=True,
bbox_inches="tight", pad_inches=0)
return ax