x = m + 2*dw
y = 20*dr
c.text(x, y,
r"""Braiding with Fibonacci anyons
can realize universal quantum computing, so
we don't expect to be able to simulate
every instance in a reasonable amount of time.
Instead we bound the compute time, and any
instance that exceeds this bound is considered
``missing'' data:""",
[text.parbox(dw-2*m),])
y -= 18*dr
try:
c.insert(epsfile.epsfile(x, y, "qip/fibonacci.eps", width=(dw-2*m)))
except IOError, e:
print e
# -------------------------------------------------------------------
the_can = canvas.canvas()
the_can.insert(c, [trafo.scale(SCALE)])
the_can.writeEPSfile("poster")
the_can.writePDFfile("poster")
def special(self, s, fontmap):
x = self.pos[_POS_H] * self.pyxconv
y = -self.pos[_POS_V] * self.pyxconv
if self.debug:
self.debugfile.write("%d: xxx '%s'\n" % (self.filepos, s))
if not s.startswith("PyX:"):
logger.warning("ignoring special '%s'" % s)
return
# it is in general not safe to continue using the currently active font because
# the specials may involve some gsave/grestore operations
self.flushtext(fontmap)
command, args = s[4:].split()[0], s[4:].split()[1:]
if command == "color_begin":
if args[0] == "cmyk":
c = color.cmyk(float(args[1]), float(args[2]), float(args[3]), float(args[4]))
elif args[0] == "gray":
c = color.gray(float(args[1]))
elif args[0] == "hsb":
c = color.hsb(float(args[1]), float(args[2]), float(args[3]))
elif args[0] == "rgb":
c = color.rgb(float(args[1]), float(args[2]), float(args[3]))
elif args[0] == "RGB":
c = color.rgb(int(args[1])/255.0, int(args[2])/255.0, int(args[3])/255.0)
elif args[0] == "texnamed":
try:
c = getattr(color.cmyk, args[1])
except AttributeError:
raise RuntimeError("unknown TeX color '%s', aborting" % args[1])
elif args[0] == "pyxcolor":
# pyx.color.cmyk.PineGreen or
# pyx.color.cmyk(0,0,0,0.0)
pat = re.compile(r"(pyx\.)?(color\.)?(?P<model>(cmyk)|(rgb)|(grey)|(gray)|(hsb))[\.]?(?P<arg>.*)")
sd = pat.match(" ".join(args[1:]))
if sd:
sd = sd.groupdict()
if sd["arg"][0] == "(":
numpat = re.compile(r"[+-]?((\d+\.\d*)|(\d*\.\d+)|(\d+))([eE][+-]\d+)?")
arg = tuple([float(x[0]) for x in numpat.findall(sd["arg"])])
try:
c = getattr(color, sd["model"])(*arg)
except TypeError or AttributeError:
raise RuntimeError("cannot access PyX color '%s' in TeX, aborting" % " ".join(args[1:]))
else:
try:
c = getattr(getattr(color, sd["model"]), sd["arg"])
except AttributeError:
raise RuntimeError("cannot access PyX color '%s' in TeX, aborting" % " ".join(args[1:]))
else:
raise RuntimeError("cannot access PyX color '%s' in TeX, aborting" % " ".join(args[1:]))
else:
raise RuntimeError("color model '%s' cannot be handled by PyX, aborting" % args[0])
self.beginsubpage([c])
elif command == "color_end":
self.endsubpage()
elif command == "rotate_begin":
self.beginsubpage([trafo.rotate_pt(float(args[0]), x, y)])
elif command == "rotate_end":
self.endsubpage()
elif command == "scale_begin":
self.beginsubpage([trafo.scale_pt(float(args[0]), float(args[1]), x, y)])
elif command == "scale_end":
self.endsubpage()
elif command == "epsinclude":
# parse arguments
argdict = {}
for arg in args:
name, value = arg.split("=")
argdict[name] = value
# construct kwargs for epsfile constructor
epskwargs = {}
epskwargs["filename"] = argdict["file"]
epskwargs["bbox"] = bbox.bbox_pt(float(argdict["llx"]), float(argdict["lly"]),
float(argdict["urx"]), float(argdict["ury"]))
if "width" in argdict:
epskwargs["width"] = float(argdict["width"]) * unit.t_pt
if "height" in argdict:
epskwargs["height"] = float(argdict["height"]) * unit.t_pt
if "clip" in argdict:
epskwargs["clip"] = int(argdict["clip"])
self.actpage.insert(epsfile.epsfile(x * unit.t_pt, y * unit.t_pt, **epskwargs))
elif command == "marker":
if len(args) != 1:
raise RuntimeError("marker contains spaces")
for c in args[0]:
if c not in string.ascii_letters + string.digits + "@":
raise RuntimeError("marker contains invalid characters")
if args[0] in self.actpage.markers:
raise RuntimeError("marker name occurred several times")
self.actpage.markers[args[0]] = x * unit.t_pt, y * unit.t_pt
else:
raise RuntimeError("unknown PyX special '%s', aborting" % command)
#ax.annotate("B", (0,1.), xycoords=(ax.get_yaxis().get_label(), "axes fraction"),
# fontsize=14)
#suptitle("Figure S%i"%sfn)
figures.append(fig)
# <codecell>
#Principles taken from http://matplotlib.1069221.n5.nabble.com/svg-in-plot-td27904.html
fig.savefig("ChildrenandTime.eps")
from pyx import canvas, epsfile
c = canvas.canvas()
# load both external files
c.insert(epsfile.epsfile(0, 0, "ChildrenandTime.eps"))
c.insert(epsfile.epsfile(4, 17, "Parent-nChild-Diagram1.eps", scale=1.4))
c.insert(epsfile.epsfile(13.5, 17, "Parent-nChild-Diagram2.eps", scale=1.4))
# save generated EPS files
c.writeEPSfile("FigureS3")
sfn+=1
# <codecell>
import matplotlib.image as mpimg
img=mpimg.imread('/data/alstottjd/Langley/Payout_diagram.png')
fig = plt.figure()
imgplot = plt.imshow(img)
def special(self, s, fontmap):
x = self.pos[_POS_H] * self.pyxconv
y = -self.pos[_POS_V] * self.pyxconv
if self.debug:
self.debugfile.write("%d: xxx '%s'\n" % (self.filepos, s))
if not s.startswith("PyX:"):
logger.warning("ignoring special '%s'" % s)
return
# it is in general not safe to continue using the currently active font because
# the specials may involve some gsave/grestore operations
self.flushtext(fontmap)
command, args = s[4:].split()[0], s[4:].split()[1:]
if command == "color_begin":
if args[0] == "cmyk":
c = color.cmyk(float(args[1]), float(args[2]), float(args[3]),
float(args[4]))
elif args[0] == "gray":
c = color.gray(float(args[1]))
elif args[0] == "hsb":
c = color.hsb(float(args[1]), float(args[2]), float(args[3]))
elif args[0] == "rgb":
c = color.rgb(float(args[1]), float(args[2]), float(args[3]))
elif args[0] == "RGB":
c = color.rgb(
int(args[1]) / 255.0,
int(args[2]) / 255.0,
int(args[3]) / 255.0)
elif args[0] == "texnamed":
try:
c = getattr(color.cmyk, args[1])
except AttributeError:
raise RuntimeError("unknown TeX color '%s', aborting" %
args[1])
elif args[0] == "pyxcolor":
# pyx.color.cmyk.PineGreen or
# pyx.color.cmyk(0,0,0,0.0)
pat = re.compile(
r"(pyx\.)?(color\.)?(?P<model>(cmyk)|(rgb)|(grey)|(gray)|(hsb))[\.]?(?P<arg>.*)"
)
sd = pat.match(" ".join(args[1:]))
if sd:
sd = sd.groupdict()
if sd["arg"][0] == "(":
numpat = re.compile(
r"[+-]?((\d+\.\d*)|(\d*\.\d+)|(\d+))([eE][+-]\d+)?"
)
arg = tuple(
[float(x[0]) for x in numpat.findall(sd["arg"])])
try:
c = getattr(color, sd["model"])(*arg)
except TypeError or AttributeError:
raise RuntimeError(
"cannot access PyX color '%s' in TeX, aborting"
% " ".join(args[1:]))
else:
try:
c = getattr(getattr(color, sd["model"]), sd["arg"])
except AttributeError:
raise RuntimeError(
"cannot access PyX color '%s' in TeX, aborting"
% " ".join(args[1:]))
else:
raise RuntimeError(
"cannot access PyX color '%s' in TeX, aborting" %
" ".join(args[1:]))
else:
raise RuntimeError(
"color model '%s' cannot be handled by PyX, aborting" %
args[0])
self.beginsubpage([c])
elif command == "color_end":
self.endsubpage()
elif command == "rotate_begin":
self.beginsubpage([trafo.rotate_pt(float(args[0]), x, y)])
elif command == "rotate_end":
self.endsubpage()
elif command == "scale_begin":
self.beginsubpage(
[trafo.scale_pt(float(args[0]), float(args[1]), x, y)])
elif command == "scale_end":
self.endsubpage()
elif command == "epsinclude":
# parse arguments
argdict = {}
for arg in args:
name, value = arg.split("=")
argdict[name] = value
# construct kwargs for epsfile constructor
epskwargs = {}
epskwargs["filename"] = argdict["file"]
epskwargs["bbox"] = bbox.bbox_pt(float(argdict["llx"]),
float(argdict["lly"]),
float(argdict["urx"]),
float(argdict["ury"]))
if "width" in argdict:
epskwargs["width"] = float(argdict["width"]) * unit.t_pt
if "height" in argdict:
epskwargs["height"] = float(argdict["height"]) * unit.t_pt
if "clip" in argdict:
epskwargs["clip"] = int(argdict["clip"])
self.actpage.insert(
epsfile.epsfile(x * unit.t_pt, y * unit.t_pt, **epskwargs))
elif command == "marker":
if len(args) != 1:
raise RuntimeError("marker contains spaces")
for c in args[0]:
if c not in string.ascii_letters + string.digits + "@":
raise RuntimeError("marker contains invalid characters")
if args[0] in self.actpage.markers:
raise RuntimeError("marker name occurred several times")
self.actpage.markers[args[0]] = x * unit.t_pt, y * unit.t_pt
else:
raise RuntimeError("unknown PyX special '%s', aborting" % command)
def plot(logn, logt, opsn, opst, pages, graphs, no_clean, debug):
fname = str(datetime.now()).replace(' ', '_')
plt.rc('font', family='Input Mono')
cwd = sys.path[0]
try:
os.mkdir(cwd + '/../tmp')
if debug > 0:
err.log('../tmp/ directory created for temporary storage.')
except FileExistsError:
if debug > 0:
err.log(
'../tmp/ directory exists; using it for temporary storage.')
new_logn = []
new_logt = []
new_pairs = set()
for i, t in enumerate(logt):
p = (t, logn[i])
if p not in new_pairs:
new_logn.append(logn[i])
new_logt.append(t)
logn = new_logn
logt = new_logt
xmax = int(max(logn))
xmin = int(min(logn))
ymax = int(max(logt))
ymin = int(min(logt))
xrng = max(xmax - xmin, 0)
yrng = max(ymax - ymin, 0)
roots = {}
t_counts = np.zeros(yrng + 1)
n_counts = np.zeros(xrng + 1)
t_pairs = set()
n_pairs = set()
ylist = range(ymin, ymax + 1)
xlist = range(xmin, xmax + 1)
xticker_base = 1.0
if xrng > ticker.MultipleLocator.MAXTICKS - 50:
xticker_base = xrng / ticker.MultipleLocator.MAXTICKS * 1.5
yticker_base = 1.0
if yrng > ticker.MultipleLocator.MAXTICKS - 50:
yticker_base = yrng / ticker.MultipleLocator.MAXTICKS * 1.5
yloc = ticker.MultipleLocator(base=yticker_base)
xloc = ticker.MultipleLocator(base=xticker_base)
fig = plt.figure(figsize=(10, 10))
fontP = FontProperties()
fontP.set_size('small')
gs = gridspec.GridSpec(2, 2)
kx = dict(aspect='auto')
ax_main = plt.subplot(gs[1, 0], **kx)
ax_count = plt.subplot(gs[1, 1], **kx)
ax_vcount = plt.subplot(gs[0, 0], **kx)
ax_none = plt.subplot(gs[0, 1], **kx)
ax_small = plt.axes([0.73, 0.11, 0.17, 0.17])
ax_main.yaxis.set_major_locator(ticker.MaxNLocator(integer=True))
ax_main.xaxis.set_major_locator(ticker.MaxNLocator(integer=True))
ax_count.yaxis.set_major_locator(ticker.MaxNLocator(integer=True))
ax_count.xaxis.set_major_locator(ticker.MaxNLocator(integer=True))
ax_vcount.yaxis.set_major_locator(ticker.MaxNLocator(integer=True))
ax_vcount.xaxis.set_major_locator(ticker.MaxNLocator(integer=True))
plt.xticks([])
plt.yticks([])
ax_small.yaxis.set_minor_locator(yloc)
ax_small.yaxis.grid(True, which='minor', color=colors.h_light_gray)
ax_small.set_axisbelow(True)
gs.update(wspace=0.00, hspace=-0.00)
log_marker = 'x'
if len(opst) > 50:
if debug > 1:
err.log('Input size is ' + str(len(opst)) + ', using marker \'o\'')
log_marker = 'o'
elif debug > 1:
err.log('Input size is ' + str(len(opst)) + ', using marker \'x\'')
if pages:
partial_logn = []
partial_logt = []
partial_opst = []
partial_opsn = []
last_logt_i = 0
logt_i = 0
for i in range(0, len(opst)):
if debug > 1:
err.log("Generating data plot number " + str(i))
partial_opst = [opst[i]]
partial_opsn = [opsn[i]]
op_t = opst[i]
last_logt_i = logt_i + 1
roots = {}
while logt_i + 1 < len(logt) and logt[logt_i + 1] <= op_t:
logt_i += 1
roots[logt[last_logt_i]] = logn[last_logt_i]
partial_logn = []
partial_logt = []
for j in range(last_logt_i, logt_i + 1):
partial_logt.append(logt[j])
partial_logn.append(logn[j])
if debug > 1:
err.log("Starting plot generation")
add_plot(fname, cwd, fig, partial_logn, partial_logt, partial_opsn,
partial_opst, t_counts, n_counts, t_pairs, n_pairs,
log_marker, xloc, yloc, ax_main, ax_count, ax_vcount,
ax_none, ax_small, xmax, xmin, ymax, ymin, xrng, yrng,
xlist, ylist, roots, graphs, i, debug)
if len(graphs) > 0:
del graphs[0]
else:
for i, t in enumerate(logt):
if t not in roots.keys():
roots[t] = logn[i]
add_plot(fname, cwd, fig, logn, logt, opsn, opst, t_counts, n_counts,
t_pairs, n_pairs, log_marker, xloc, yloc, ax_main, ax_count,
ax_vcount, ax_none, ax_small, xmax, xmin, ymax, ymin, xrng,
yrng, xlist, ylist, roots, graphs, 0, debug)
plt.close()
page_list = []
page_size = document.paperformat(200, 200)
num_plots = 1
if pages:
num_plots = len(opsn)
for i in range(0, num_plots):
if debug > 0:
err.log("Concatenating PS pages for plot #" + str(i))
plots_name = cwd + '/../tmp/' + fname + '_' + str(i) + '.eps'
tree_name = cwd + '/../tmp/' + fname + '_' + str(i) + '.gv.eps'
got_tree = True
try:
tree_file = open(tree_name, 'r')
tree_w = 0
tree_h = 0
for line in tree_file:
if line.startswith("%%BoundingBox:"):
bbline = line.split()
tree_w = bbline[3]
tree_h = bbline[4]
if debug > 1:
err.log(
"In EPS #{} got height: {} and width {} from line {}"
.format(i, tree_h, tree_w, line.replace('\n', '')))
break
else:
err.err(
"BoundingBox line not found in EPS file for tree diagram.")
tree_file.close()
except:
got_tree = False
c = canvas.canvas()
plots_file = epsfile.epsfile(0, 0, plots_name, height=160, width=160)
c.insert(plots_file)
if got_tree:
if tree_w > tree_h:
tree_file = epsfile.epsfile(120,
120,
tree_name,
align='cc',
width=70)
else:
tree_file = epsfile.epsfile(120,
120,
tree_name,
align='cc',
height=70)
c.insert(tree_file)
p = document.page(c,
fittosize=True,
centered=True,
paperformat=page_size)
if no_clean:
c.writeEPSfile(cwd + '/../tmp/' + fname + '_' + str(i) +
'.zipped.eps')
page_list.append(p)
d = document.document(page_list)
out_name = cwd + '/../outputs/' + fname + '.ps'
if debug > 0:
err.log("Saving final output " + out_name)
d.writePSfile(out_name)
if not no_clean:
for tmpf in os.listdir(cwd + '/../tmp/'):
os.remove(cwd + '/../tmp/' + tmpf)
os.rmdir(cwd + '/../tmp/')