def corner(nx, ny, z, facecolor, edgecolor, trans, xdir, ydir):
if xdir:
p = path.path(path.moveto(*projector(nx, z, ny)),
path.lineto(*projector(nx - 1, z, ny)),
path.lineto(*projector(nx - 1, z + 1, ny)),
path.lineto(*projector(nx, z + 1, ny)), path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
if ydir:
p = path.path(path.moveto(*projector(nx, z, ny)),
path.lineto(*projector(nx, z, ny + 1)),
path.lineto(*projector(nx, z + 1, ny + 1)),
path.lineto(*projector(nx, z + 1, ny)), path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
x0, y0 = projector(nx, z, ny)
x1, y1 = projector(nx, z + 1, ny)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
def server(r, servercolor=color.rgb(0.5, 0.5, 0.8), transparency=0):
c = canvas.canvas()
c.fill(path.circle(0, 0, r), [
servercolor,
color.transparency(transparency),
trafo.scale(1, 0.5).translated(0, 0.5 * r)
])
h = 2 * r
p = path.path(path.moveto(-r, 0), path.lineto(-r, -h),
path.arc(0, -h, r, 180, 0), path.lineto(r, 0),
path.arcn(0, 0, r, 0, 180), path.closepath())
c.fill(p, [
servercolor,
color.transparency(transparency),
trafo.scale(1, 0.5).translated(0, 0.5 * r - 0.08 * r)
])
return c
def timeslice(x, y, transparency=0.0, label="", W=3):
dopath(
[(-1.1, y0), (-0.1, y1), (W + 0.2, y1), (W - 0.8, y0)],
fill=[shade, color.transparency(0.3)],
extra=[trafo.translate(x, y)],
closepath=True,
)
if label:
c.text(W + 0.2, 0.0, label, west + [trafo.translate(x, y)])
def corner(nx, ny, z, facecolor, edgecolor, trans, xdir, ydir):
if xdir:
p = path.path(path.moveto(*projector(nx, z, ny)),
path.lineto(*projector(nx-1, z, ny)),
path.lineto(*projector(nx-1, z+1, ny)),
path.lineto(*projector(nx, z+1, ny)),
path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
if ydir:
p = path.path(path.moveto(*projector(nx, z, ny)),
path.lineto(*projector(nx, z, ny+1)),
path.lineto(*projector(nx, z+1, ny+1)),
path.lineto(*projector(nx, z+1, ny)),
path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
x0, y0 = projector(nx, z, ny)
x1, y1 = projector(nx, z+1, ny)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
def loop(x0, y0, r1, theta0, theta1, tpy):
t = Turtle(x0, y0, theta0)
#theta = 0.55*pi
theta = theta1
r2 = 2*r1*sin(theta - 0.5*pi)
t.penup().fwd(0.1*r1).pendown()
t.fwd(0.9*r1).right(theta).fwd(r2).right(theta).fwd(0.9*r1)
t.stroke([deco.earrow(),
deformer.smoothed(4.0), style.linewidth.Thick,
color.transparency(tpy), tr])
def frontplane(z, nxmax, mymax, facecolor, edgecolor, trans):
p = path.path(path.moveto(*projector(0, z, 0)),
path.lineto(*projector(nxmax, z, 0)),
path.lineto(*projector(nxmax, z, nymax)),
path.lineto(*projector(0, z, nymax)), path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
c.stroke(p, [edgecolor])
for nx in range(1, nxmax):
x0, y0 = projector(nx, z, 0)
x1, y1 = projector(nx, z, nymax)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
for ny in range(1, nymax):
x0, y0 = projector(0, z, ny)
x1, y1 = projector(nxmax, z, ny)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
def frontplane(z, nxmax, mymax, facecolor, edgecolor, trans):
p = path.path(path.moveto(*projector(0, z, 0)),
path.lineto(*projector(nxmax, z, 0)),
path.lineto(*projector(nxmax, z, nymax)),
path.lineto(*projector(0, z, nymax)),
path.closepath())
c.fill(p, [facecolor, color.transparency(trans)])
c.stroke(p, [edgecolor])
for nx in range(1, nxmax):
x0, y0 = projector(nx, z, 0)
x1, y1 = projector(nx, z, nymax)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
for ny in range(1, nymax):
x0, y0 = projector(0, z, ny)
x1, y1 = projector(nxmax, z, ny)
c.stroke(path.line(x0, y0, x1, y1), [edgecolor])
c.insert(c_m1)
c.insert(c_m2, [trafo.translate(c_m1.bbox().width() + 0.1, 0)])
end = c_m1.bbox().right() + c_m2.bbox().width() + 0.1
dist2 = 0.6
c.insert(c_m3, [trafo.translate(end + dist2 - c_m3.bbox().left(), 0)])
ycenter = 0.5 * (c_m1.bbox().top() + c_m1.bbox().bottom())
for dy in (-0.05, 0.05):
c.stroke(
path.line(end + 0.15, ycenter + dy, end + dist2 - 0.15, ycenter + dy))
c_tot = canvas.canvas()
for y in range(4):
c_tot.insert(c, [trafo.translate(0, 1.5 * y)])
dx = 0.2
colorprops = [color.rgb(0.8, 0.2, 0), color.transparency(0.2)]
arrowprops = [deco.earrow] + colorprops
for lineno, (ny, nx) in enumerate(product((0, 1), repeat=2)):
yoff = 1.5 * (3 - lineno) + 0.17
c_tot.stroke(path.line(-dx, yoff - 0.5 * ny, 0.5 + dx, yoff - 0.5 * ny),
arrowprops)
xoff = c_m1.bbox().width() + 0.1 + 0.5 * nx
c_tot.stroke(path.line(xoff, yoff + 0.2, xoff, yoff - 0.7), arrowprops)
wd = 0.6
ht = 0.5
xoff = end + dist2 - c_m3.bbox().left() + 0.7 * nx
c_tot.stroke(
path.rect(xoff - 0.5 * wd, yoff - 0.5 * ny - 0.5 * ht, wd, ht),
colorprops)
c_tot.writePDFfile()
def draw_continent_circle(con,
name="",
draw_upper_landscape=True,
draw_lower_landscape=False,
draw_upper_green=True,
draw_lower_purple=False,
draw_train_tracks=False,
draw_foliation=True,
foliation_style_old=False,
foliation_style_split=False,
foliation_style_cusp_leaves=True,
foliation_style_boundary_leaves=True,
shade_triangles=False,
draw_fund_domain=False,
fund_dom_tets=None,
draw_fund_domain_edges=False,
draw_tetrahedron_rectangles=[]):
global_scale_up = 10.0
edge_thickness = 0.02
track_thickness = 0.02
leaf_thickness = 0.03
edge_colours = {
True: color.rgb(0.9, 0.3, 0),
False: color.rgb(0, 0.3, 0.9)
}
green = color.rgb(0.0, 0.5, 0.0)
purple = color.rgb(0.5, 0.0, 0.5)
scl = trafo.trafo(matrix=((global_scale_up, 0), (0, global_scale_up)),
vector=(0, 0))
canv = canvas.canvas()
canv.stroke(path.circle(0, 0, global_scale_up), [style.linewidth(0.02)])
n = len(con.coast)
for v in con.coast:
i = v.coastal_index
t = 2 * pi * float(i) / float(n)
v.circle_pos = complex(cos(t), sin(t))
vert_pos = v.circle_pos * 1.01 * global_scale_up
canv.text(vert_pos.real,
vert_pos.imag,
"$" + str(con.vertices.index(v)) + "$",
textattrs=[
text.size(-4), text.halign.left, text.valign.middle,
trafo.rotate(
(180 / pi) * atan2(vert_pos.imag, vert_pos.real))
])
# vert_pos2 = v.circle_pos * 1.2 * global_scale_up
# p = path.path(path.moveto(vert_pos.real, vert_pos.imag), path.lineto(vert_pos2.real, vert_pos2.imag))
# canv.stroke(p, [deco.curvedtext("$"+str(con.vertices.index(v))+"$")])
### highlight vertices of tetrahedra in a fundamental domain
if draw_fund_domain:
if fund_dom_tets == None:
fund_dom_tets = get_fund_domain_tetrahedra(con)
for con_tet in fund_dom_tets:
if type(
con_tet
) == continent_tetrahedron: ### could be an integer if we didnt find this tet
if draw_fund_domain_edges:
for e in con_tet.edges():
col = edge_colours[e.is_red]
u, v = e.vertices
p = make_arc(u.circle_pos, v.circle_pos)
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(edge_thickness),
style.linecap.round, col
])
update_fund_dom_tet_nums(con, fund_dom_tets)
for v in [v for v in con.coast if v.fund_dom_tet_nums != []]:
vert_pos = v.circle_pos * 1.03 * global_scale_up
canv.text(vert_pos.real,
vert_pos.imag,
"$" + str(v.fund_dom_tet_nums) + "$",
textattrs=[
text.size(-4), text.halign.left, text.valign.middle,
trafo.rotate(
(180 / pi) * atan2(vert_pos.imag, vert_pos.real))
])
# lower_colours = {True: color.rgb(0.5,0.3,0), False: color.rgb(0,0.3,0.5)}
# upper_colours = {True: color.rgb(0.9,0.3,0), False: color.rgb(0,0.3,0.9)}
landscape_edges = [con.lower_landscape_edges, con.upper_landscape_edges]
# colours = [lower_colours, upper_colours]
upper_tris = con.upper_landscape_triangles
lower_tris = con.lower_landscape_triangles
boundary_tris = [lower_tris, upper_tris]
if shade_triangles:
u, v, w = con.triangle_path[0].vertices
p = make_arc(u.circle_pos, v.circle_pos)
q = make_arc(v.circle_pos, w.circle_pos)
r = make_arc(w.circle_pos, u.circle_pos)
p.append(q[1])
p.append(r[1]) ### remove extraneous moveto commands
p = p.transformed(scl)
canv.stroke(
p, [deco.filled([color.transparency(0.8)]),
style.linewidth(0)])
u, v, w = con.triangle_path[-1].vertices
p = make_arc(u.circle_pos, v.circle_pos)
q = make_arc(v.circle_pos, w.circle_pos)
r = make_arc(w.circle_pos, u.circle_pos)
p.append(q[1])
p.append(r[1]) ### remove extraneous moveto commands
p = p.transformed(scl)
canv.stroke(
p, [deco.filled([color.transparency(0.8)]),
style.linewidth(0)])
# for triangle in con.triangle_path:
# u,v,w = triangle.vertices
# p = make_arc(u.circle_pos, v.circle_pos)
# q = make_arc(v.circle_pos, w.circle_pos)
# r = make_arc(w.circle_pos, u.circle_pos)
# p.append(q[1])
# p.append(r[1]) ### remove extraneous moveto commands
# p = p.transformed(scl)
# canv.stroke(p, [deco.filled([color.transparency(0.8)]), style.linewidth(0)])
to_do = []
if draw_lower_landscape:
to_do.append(0)
if draw_upper_landscape:
to_do.append(1)
for i in to_do:
for e in landscape_edges[i]:
col = edge_colours[e.is_red]
transp = []
if i == 0:
transp = [color.transparency(0.75)]
u, v = e.vertices
p = make_arc(u.circle_pos, v.circle_pos)
p = p.transformed(scl)
canv.stroke(
p,
[style.linewidth(edge_thickness), style.linecap.round, col] +
transp)
for tri in boundary_tris[i]:
center = incenter(tri.vertices[0].circle_pos,
tri.vertices[1].circle_pos,
tri.vertices[2].circle_pos)
# canv.fill(path.circle(global_scale_up*center[0], global_scale_up*center[1], 0.1))
canv.text(global_scale_up * center[0],
global_scale_up * center[1],
"$" + str(tri.index) + "$",
textattrs=[
text.size(-2), text.halign.center, text.valign.middle
] + transp)
### train tracks...
purple_train_routes = [
] ### pairs of coastal edges corresponding to a train route
green_train_routes = []
if draw_lower_purple:
if draw_train_tracks:
for tri in lower_tris:
midpts = []
is_reds = []
for e in tri.edges:
is_reds.append(e.is_red)
u, v = e.vertices
p, midpt = make_arc(u.circle_pos,
v.circle_pos,
return_midpt=True)
midpts.append(midpt)
for i in range(3):
if (is_reds[i] == is_reds[(i + 1) % 3]) or (
not is_reds[i] and is_reds[(i + 1) % 3]):
p = make_arc(midpts[i], midpts[(i + 1) % 3])
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(track_thickness),
style.linecap.round, purple
])
if draw_foliation:
for edge in con.lower_landscape_edges:
leaf_end_edges = []
if edge.is_coastal():
if not edge.is_coastal_sink(upper=False):
leaf_end_edges.append(edge)
for tri in edge.boundary_triangles:
if not tri.is_upper:
last_tri = con.flow(tri)[0]
last_edge = last_tri.edges[
last_tri.downriver_index()]
leaf_end_edges.append(last_edge)
else:
if edge.is_watershed():
for tri in edge.boundary_triangles:
last_tri = con.flow(tri)[0]
last_edge = last_tri.edges[
last_tri.downriver_index()]
leaf_end_edges.append(last_edge)
if len(leaf_end_edges) == 2:
purple_train_routes.append(leaf_end_edges)
if foliation_style_old:
leaf_ends = []
for e in leaf_end_edges:
endpts = e.vertices
_, midpt = make_arc(endpts[0].circle_pos,
endpts[1].circle_pos,
return_midpt=True)
leaf_ends.append(midpt)
p = make_arc(leaf_ends[0], leaf_ends[1])
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(leaf_thickness),
style.linecap.round, purple
])
if draw_upper_green:
if draw_train_tracks:
for tri in upper_tris:
midpts = []
is_reds = []
for e in tri.edges:
is_reds.append(e.is_red)
u, v = e.vertices
p, midpt = make_arc(u.circle_pos,
v.circle_pos,
return_midpt=True)
midpts.append(midpt)
for i in range(3):
if (is_reds[i] == is_reds[(i + 1) % 3]) or (
is_reds[i] and not is_reds[(i + 1) % 3]):
p = make_arc(midpts[i], midpts[(i + 1) % 3])
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(track_thickness),
style.linecap.round, green
])
if draw_foliation:
for edge in con.upper_landscape_edges:
leaf_end_edges = []
if edge.is_coastal():
if not edge.is_coastal_sink(upper=True):
leaf_end_edges.append(edge)
for tri in edge.boundary_triangles:
if tri.is_upper:
last_tri = con.flow(tri)[0]
last_edge = last_tri.edges[
last_tri.downriver_index()]
leaf_end_edges.append(last_edge)
else:
if edge.is_watershed():
for tri in edge.boundary_triangles:
last_tri = con.flow(tri)[0]
last_edge = last_tri.edges[
last_tri.downriver_index()]
leaf_end_edges.append(last_edge)
if len(leaf_end_edges) == 2:
green_train_routes.append(leaf_end_edges)
if foliation_style_old:
leaf_ends = []
for e in leaf_end_edges:
endpts = e.vertices
_, midpt = make_arc(endpts[0].circle_pos,
endpts[1].circle_pos,
return_midpt=True)
leaf_ends.append(midpt)
p = make_arc(leaf_ends[0], leaf_ends[1])
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(leaf_thickness),
style.linecap.round, green
])
if draw_foliation and (foliation_style_split or foliation_style_cusp_leaves
or foliation_style_boundary_leaves):
for e in con.coastal_edges:
e.purple_ends = []
e.green_ends = []
for e1, e2 in purple_train_routes:
e1.purple_ends.append(e2)
e2.purple_ends.append(e1)
for e1, e2 in green_train_routes:
e1.green_ends.append(e2)
e2.green_ends.append(e1)
for i, e in enumerate(con.coastal_edges):
rotated_coastal_edges = con.coastal_edges[
i:] + con.coastal_edges[:i]
e.purple_ends.sort(
key=lambda e_other: rotated_coastal_edges.index(e_other),
reverse=True)
e.green_ends.sort(
key=lambda e_other: rotated_coastal_edges.index(e_other),
reverse=True)
if e.is_red:
e.ends = e.green_ends + e.purple_ends
else:
e.ends = e.purple_ends + e.green_ends
if foliation_style_split:
for e1, e2 in purple_train_routes:
p1 = end_pos(e2, e1)
p2 = end_pos(e1, e2)
p = make_arc(p1, p2)
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(leaf_thickness), style.linecap.round,
purple
])
for e1, e2 in green_train_routes:
p1 = end_pos(e2, e1)
p2 = end_pos(e1, e2)
p = make_arc(p1, p2)
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(leaf_thickness), style.linecap.round, green
])
if foliation_style_cusp_leaves or foliation_style_boundary_leaves:
for i, c in enumerate(con.coast):
c.purple_thorn_end_positions = [] ### complex numbers
c.purple_thorn_ends = [
] ### [coastal arc, position along that arc]
e = con.coastal_edges[i]
e1 = e.purple_ends[0]
while True:
index = e1.purple_ends.index(e)
if index == len(e1.purple_ends) - 1:
break
else:
c.purple_thorn_end_positions.append(
end_pos(e, e1, offset=0.5))
c.purple_thorn_ends.append((e1, e1.ends.index(e)))
e, e1 = e1, e1.purple_ends[index + 1]
if foliation_style_boundary_leaves:
e_before = con.coastal_edges[(i - 1) % len(con.coast)]
e_after = con.coastal_edges[i]
first_pos = end_pos(e_after.purple_ends[0],
e_after,
offset=-0.25)
last_pos = end_pos(e_before.purple_ends[-1],
e_before,
offset=0.25)
c.purple_thorn_end_positions = [
first_pos
] + c.purple_thorn_end_positions + [last_pos]
arcs = []
for i in range(len(c.purple_thorn_end_positions) - 1):
arcs.append(
make_arc(c.purple_thorn_end_positions[i],
c.purple_thorn_end_positions[i + 1]))
for p in arcs:
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(leaf_thickness),
style.linecap.round, purple
])
if foliation_style_cusp_leaves:
for thorn_end in c.purple_thorn_ends:
thorn_end_pos = end_pos2(thorn_end)
p = make_arc(c.circle_pos, thorn_end_pos)
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(leaf_thickness),
style.linecap.round, purple
])
for i, c in enumerate(con.coast):
c.green_thorn_end_positions = [] ### complex numbers
c.green_thorn_ends = [
] ### [coastal arc, position along that arc]
e = con.coastal_edges[i]
e1 = e.green_ends[0]
while True:
index = e1.green_ends.index(e)
if index == len(e1.green_ends) - 1:
break
else:
c.green_thorn_end_positions.append(
end_pos(e, e1, offset=0.5))
c.green_thorn_ends.append((e1, e1.ends.index(e)))
e, e1 = e1, e1.green_ends[index + 1]
if foliation_style_boundary_leaves:
e_before = con.coastal_edges[(i - 1) % len(con.coast)]
e_after = con.coastal_edges[i]
first_pos = end_pos(e_after.green_ends[0],
e_after,
offset=-0.25)
last_pos = end_pos(e_before.green_ends[-1],
e_before,
offset=0.25)
c.green_thorn_end_positions = [
first_pos
] + green_thorn_end_positions + [last_pos]
arcs = []
for i in range(len(c.green_thorn_end_positions) - 1):
arcs.append(
make_arc(c.green_thorn_end_positions[i],
c.green_thorn_end_positions[i + 1]))
for p in arcs:
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(leaf_thickness),
style.linecap.round, green
])
if foliation_style_cusp_leaves:
for thorn_end in c.green_thorn_ends:
thorn_end_pos = end_pos2(thorn_end)
p = make_arc(c.circle_pos, thorn_end_pos)
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(leaf_thickness),
style.linecap.round, green
])
for tet in draw_tetrahedron_rectangles:
purple_sides = tet_purple_rectangle_sides(
tet, actually_do_green=False)
green_sides = tet_purple_rectangle_sides(
tet, actually_do_green=True)
for side in purple_sides:
for cusp_leaf in side:
if cusp_leaf != None:
v, thorn_end = cusp_leaf
thorn_end_pos = end_pos2(thorn_end)
p = make_arc(v.circle_pos, thorn_end_pos)
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(2 * leaf_thickness),
style.linecap.round, purple
])
for side in green_sides:
for cusp_leaf in side:
if cusp_leaf != None:
v, thorn_end = cusp_leaf
thorn_end_pos = end_pos2(thorn_end)
p = make_arc(v.circle_pos, thorn_end_pos)
p = p.transformed(scl)
canv.stroke(p, [
style.linewidth(2 * leaf_thickness),
style.linecap.round, green
])
output_filename = 'Images/CircleContinent/' + name + '.pdf'
canv.writePDFfile(output_filename)
unit.set(xscale=1.2, wscale=1.5)
frontplane = canvas.canvas()
backplane = canvas.canvas()
xcells = 4
ycells = 3
xshift = 0.8
yshift = 1.2
dist = 0.2
myred = color.rgb(0.8, 0, 0)
mygreen = color.rgb(0, 0.6, 0)
myblue = color.rgb(0, 0, 0.8)
for c, start in ((frontplane, 0), (backplane, xcells * ycells)):
c.stroke(
path.rect(0, 0, 4, 3),
[deco.filled([color.grey(1), color.transparency(0.2)])])
for x in range(1, xcells):
c.stroke(path.line(x, 0, x, ycells))
for y in range(1, ycells):
c.stroke(path.line(0, y, xcells, y))
for entry in range(xcells * ycells):
x = entry % 4
y = ycells - entry // 4
c.text(x + 0.5, y - 0.5, str(start + entry),
[text.halign.center, text.valign.middle])
c = canvas.canvas()
c.insert(backplane, [trafo.translate(xshift, yshift)])
for x, y in product((0, xcells), (0, ycells)):
c.stroke(path.line(x, y, x + xshift, y + yshift))
c.insert(frontplane)
dx = -dist * yshift / sqrt(xshift**2 + yshift**2)
def plot_scores(self,
fname,
binsize=10000,
show_lads=False,
show_dips=False,
show_means=False,
show_partitions=False):
"""Plot a PDF of score data with optional indicators of partitions, "
partition means, LADs, and DIPs."""
# Make sure that the PYX module is available
try:
from pyx import canvas, path, document, color, text, style
except ImportError:
self.logger.warn("The package pyx must be installed to plot data")
return None
# Make sure desired data is present
if self.focus != 'binned':
if (self.data is None or numpy.nanmin(self.data['score']) == 0):
self.logger.warn("Requested data is not available for "
"plotting")
return None
elif (self.binned is None or numpy.nanmin(self.binned['score']) == 0):
self.logger.warn("Requested binned data is not available for "
"plotting")
return None
self.logger.info("Plotting data")
# Determine which data to use
if self.focus == 'binned':
data = self.binned
chr_indices = self.bin_indices
else:
data = self.data
chr_indices = self.chr_indices
# Plot each chromosome on its own page
pages = []
for i in range(self.chroms.shape[0]):
valid = numpy.where(
numpy.logical_not(
numpy.isnan(
data['score'][chr_indices[i]:chr_indices[i + 1]])))[0]
valid += chr_indices[i]
# Skip chromosomes without valid data
if valid.shape[0] == 0:
continue
mids = (data['coords'][valid, 0] + data['coords'][valid, 1]) // 2
if binsize > 0:
# Bin data to the resolution requested
start = (mids[0] // binsize) * binsize
stop = (mids[-1] // binsize + 1) * binsize
indices = (mids - start) // binsize
counts = numpy.bincount(indices)
Ys = numpy.bincount(
indices, weights=data['score'][valid]) / numpy.maximum(
1, counts)
mids = (start + numpy.arange(
(stop - start) // binsize) * binsize + binsize / 2)
valid = numpy.where(counts > 0)[0]
Ys = Ys[valid]
mids = mids[valid]
coords = numpy.zeros((Ys.shape[0], 2), dtype=numpy.float64)
coords[:, 0] = start + valid * binsize
coords[:, 1] = start + valid * binsize + binsize
else:
Ys = data['score'][valid]
start = data['coords'][valid, 0]
stop = data['coords'][valid[-1], 1]
coords = data['coords'][valid, :].astype(numpy.float64)
c = canvas.canvas()
width = (stop - start) / 5000000.
height = 5.
maxscore = numpy.amax(numpy.abs(Ys))
if show_means and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
maxscore = max(
maxscore,
numpy.amax(numpy.abs(self.partitions['score'][where])))
Ys /= maxscore
Ys *= height * 0.5
Xs = (mids - start) / float(stop - start) * width
coords -= start
coords /= (stop - start)
coords *= width
lpath = path.path(path.moveto(0, 0))
for j in range(valid.shape[0]):
if j == 0 or valid[j] - valid[j - 1] > 1:
lpath.append(path.lineto(coords[j, 0], 0))
lpath.append(path.lineto(Xs[j], Ys[j]))
if j == Xs.shape[0] - 1 or valid[j + 1] - valid[j] > 1:
lpath.append(path.lineto(coords[j, 1], 0))
lpath.append(path.lineto(width, 0))
lpath.append(path.closepath())
# add lads if requests and already determined
if show_lads and self.LADs is not None:
where = numpy.where(self.LADs['chr'] == i)[0]
if where.shape[0] == 0:
continue
for j in where:
X0 = ((self.LADs['coords'][j, 0] - start) /
float(stop - start) * width)
X1 = ((self.LADs['coords'][j, 1] - start) /
float(stop - start) * width)
c.fill(path.rect(X0, -height / 2, X1 - X0, height),
[color.gray(0.85)])
# add dips if requests and already determined
if show_dips and self.DIPs is not None:
print(self.DIPs.shape)
where = numpy.where(self.DIPs['chr'] == i)[0]
if where.shape[0] == 0:
continue
for j in where:
X0 = ((self.DIPs['coords'][j, 0] - start) /
float(stop - start) * width)
X1 = ((self.DIPs['coords'][j, 1] - start) /
float(stop - start) * width)
c.fill(path.rect(X0, -height / 2, X1 - X0, height),
[color.rgb.red])
# add signal track
c.fill(lpath)
c.stroke(path.line(0, -height / 2, width, -height / 2))
# add partition mean line if requested and already determined
if show_means and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
coords = ((self.partitions['coords'][where, :] - start) /
float(stop - start) * width)
Ys = ((self.partitions['score'][where] / maxscore) * height *
0.5)
lpath = path.path(path.moveto(0, 0))
for j in range(Ys.shape[0]):
if j == 0 or coords[j, 0] != coords[j - 1, 1]:
lpath.append(path.lineto(coords[j, 0], 0))
lpath.append(path.lineto(coords[j, 0], Ys[j]))
lpath.append(path.lineto(coords[j, 1], Ys[j]))
if (j == Ys.shape[0] - 1
or coords[j, 1] != coords[j + 1, 0]):
lpath.append(path.lineto(coords[j, 1], 0))
lpath.append(path.lineto(width, 0))
c.stroke(lpath, [
color.rgb.blue, style.linewidth.THIN,
color.transparency(0.5)
])
# add partition lines if requested and already determined
if show_partitions and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
coords = ((self.partitions['coords'][where, :] - start) /
float(stop - start) * width)
for j in range(coords.shape[0] - 1):
c.stroke(
path.line(coords[j, 1], -height * 0.5, coords[j, 1],
height * 0.5), [style.linewidth.THin])
if coords[j, 1] != coords[j + 1, 0]:
c.stroke(
path.line(coords[j + 1, 0], -height * 0.5,
coords[j + 1, 0], height * 0.5),
[style.linewidth.THin])
# add coordinates
for j in range(int(numpy.ceil(start / 10000000.)),
int(numpy.floor(stop / 10000000.) + 1)):
X = (j * 10000000. - start) / (stop - start) * width
c.stroke(path.line(X, -height / 2, X, -height / 2 - 0.2))
c.text(X, -height / 2 - 0.25, "%i Mb" % (j * 10),
[text.halign.center, text.valign.top])
c.text(width * 0.5, -height / 2 - 0.6,
"%s" % self.chroms[i].replace('_', ' '),
[text.halign.center, text.valign.top])
pages.append(document.page(c))
doc = document.document(pages)
doc.writePDFfile(fname)
def dorect(x, y, W=2, H=0.6):
dopath([(x-1.1, y-H), (x-0.1, y+H), (x+W+.2, y+H), (x+W-0.8, y-H)],
fill=[shade, color.transparency(0.3)],
closepath=True)
from pyx import canvas, color, deformer, path, text, trafo, unit
text.set(text.LatexRunner)
text.preamble(r'''\usepackage[scaled=0.85,lining]{FiraMono}
\usepackage[utf8]{inputenc}''')
pistring = '3.14159265358979323846264338327950288419716939937510582097494459230781640628620899862803482534211706798214808651328230664709384460955058223172535940812848111745028410270193852'
char_per_line = 25
pistring = ' '.join(
[pistring[n * char_per_line:(n + 1) * char_per_line] for n in range(10)])
unit.set(xscale=1.45)
c = canvas.canvas()
dx = 0.3
h = 4
w = 6.5
p = path.rect(-dx, -dx, w + 2 * dx, h + 2 * dx)
p = deformer.smoothed(0.5).deform(p)
c.fill(p, [color.grey(0.5), trafo.translate(0.05, -0.05)])
c.fill(p, [color.grey(0.9)])
c.text(0, 0, r'\noindent\texttt{{{}}}'.format(pistring),
[text.valign.bottom, text.parbox(5)])
c.text(0.5 * w, 0.5 * h, r'\Huge $\pi$', [
text.halign.center, text.valign.middle,
color.hsb(0.66, 0.8, 1),
color.transparency(0.2),
trafo.scale(5.8)
])
c.writePDFfile()
text.preamble(r'\usepackage[sfdefault,scaled=.85,lining]{FiraSans}\usepackage{newtxsf}')
unit.set(xscale=1.6, wscale=1.5)
frontplane = canvas.canvas()
backplane = canvas.canvas()
xcells = 4
ycells = 3
xshift = 0.8
yshift = 1.2
dist = 0.2
myred = color.rgb(0.8, 0, 0)
mygreen = color.rgb(0, 0.6, 0)
myblue = color.rgb(0, 0, 0.8)
for c, start in ((frontplane, 0), (backplane, xcells*ycells)):
c.stroke(path.rect(0, 0, 4, 3),
[deco.filled([color.grey(1), color.transparency(0.2)])])
for x in range(1, xcells):
c.stroke(path.line(x, 0, x, ycells))
for y in range(1, ycells):
c.stroke(path.line(0, y, xcells, y))
for entry in range(xcells*ycells):
x = entry % 4
y = ycells - entry // 4
c.text(x+0.5, y-0.5, str(start+entry),
[text.halign.center, text.valign.middle])
c = canvas.canvas()
c.insert(backplane, [trafo.translate(xshift, yshift)])
for x, y in product((0, xcells), (0, ycells)):
c.stroke(path.line(x, y, x+xshift, y+yshift))
c.insert(frontplane)
dx = -dist*yshift/sqrt(xshift**2+yshift**2)
c_m2 = matrix_22(m2)
m3 = np.dot(m1, m2)
c_m3 = matrix_22(m3, dx=0.7)
c.insert(c_m1)
c.insert(c_m2, [trafo.translate(c_m1.bbox().width()+0.1, 0)])
end = c_m1.bbox().right()+c_m2.bbox().width()+0.1
dist2 = 0.6
c.insert(c_m3, [trafo.translate(end+dist2-c_m3.bbox().left(), 0)])
ycenter = 0.5*(c_m1.bbox().top()+c_m1.bbox().bottom())
for dy in (-0.05, 0.05):
c.stroke(path.line(end+0.15, ycenter+dy,
end+dist2-0.15, ycenter+dy))
c_tot = canvas.canvas()
for y in range(4):
c_tot.insert(c, [trafo.translate(0, 1.5*y)])
dx = 0.2
colorprops = [color.rgb(0.8, 0.2, 0), color.transparency(0.2)]
arrowprops = [deco.earrow]+colorprops
for lineno, (ny, nx) in enumerate(product((0, 1), repeat=2)):
yoff = 1.5*(3-lineno)+0.17
c_tot.stroke(path.line(-dx, yoff-0.5*ny, 0.5+dx, yoff-0.5*ny), arrowprops)
xoff = c_m1.bbox().width()+0.1+0.5*nx
c_tot.stroke(path.line(xoff, yoff+0.2, xoff, yoff-0.7), arrowprops)
wd = 0.55
ht = 0.45
xoff = end+dist2-c_m3.bbox().left()+0.7*nx
c_tot.stroke(path.rect(xoff-0.5*wd, yoff-0.5*ny-0.5*ht, wd, ht), colorprops)
c_tot.writePDFfile()
pyplot.plot(t, )
pyplot.show()
quit()
from pyx import canvas, graph, text, color, style, trafo, unit
from pyx.graph import axis, key
text.set(mode="latex")
text.preamble(r"\usepackage{txfonts}")
figwidth = 12
gkey = key.key(pos=None, hpos=0.05, vpos=0.8)
xaxis = axis.linear(title=r"Time, \(t\)")
yaxis = axis.linear(title="Signal", min=-5, max=17)
g = graph.graphxy(width=figwidth, x=xaxis, y=yaxis, key=gkey)
plotdata = [graph.data.values(x=t, y=signal+offset, title=label) for label, signal, offset in (r"\(A(t) = \mathrm{square}(2\pi t/T)\)", A, 2.5), (r"\(B(t) = \mathrm{sawtooth}(\phi + 2 \pi t/T)\)", B, -2.5)]
linestyles = [style.linestyle.solid, style.linejoin.round, style.linewidth.Thick, color.gradient.Rainbow, color.transparency(0.5)]
plotstyles = [graph.style.line(linestyles)]
g.plot(plotdata, plotstyles)
g.plot(graph.data.values(x=t, y=listX, title="Blah"), plotstyles)
g.text(10*unit.x_pt, 0.56*figwidth, r"\textbf{Cross correlation of noisy anharmonic signals}")
g.text(10*unit.x_pt, 0.33*figwidth, "Phase shift: input \(\phi = %.2f \,\pi\), recovered \(\phi = %.2f \,\pi\)" % (phase_shift/pi, recovered_phase_shift/pi))
xxaxis = axis.linear(title=r"Time Lag, \(\Delta t\)", min=-1.5, max=1.5)
yyaxis = axis.linear(title=r"\(A(t) \star B(t)\)")
gg = graph.graphxy(width=0.2*figwidth, x=xxaxis, y=yyaxis)
plotstyles = [graph.style.line(linestyles + [color.rgb(0.2,0.5,0.2)])]
#gg.plot(graph.data.values(x=dt, y=xcorr), plotstyles)
gg.plot(graph.data.values(x=dt, y=xcorr, title="Blah"), plotstyles)
gg.stroke(gg.xgridpath(recovered_time_shift), [style.linewidth.THIck, color.gray(0.5), color.transparency(0.7)])
ggtrafos = [trafo.translate(0.75*figwidth, 0.45*figwidth)]
g.insert(gg, ggtrafos)
g.writePDFfile("so-xcorr-pyx")
[pyx.trafo.scale(0.7), pyx.trafo.rotate(ang)] + mycolor)
#####
#
# New part 12 Apr 2009 - a multitude of lines on the thermodynamics graphs
# Modified 11 May 2009 for turbulence runs
#
#####
if varstring.startswith("not implemented yet - 24 May 2010"):
# if varstring.startswith("n-T"):
from pyx.style import linestyle, linewidth
from pyx.color import transparency, rgb
from pyx.graph.style import line
from pyx.graph import data
line.defaultlineattrs += [linewidth.thick, transparency(0.5)]
myred = rgb(0.5, 0.0, 0.0)
mygreen = rgb(0.0, 0.5, 0.0)
myblue = rgb(0.0, 0.0, 0.5)
# # Free-fall time < 1.e5 years
# g.plot(data.function("x(y) = 5.31"), [line([linestyle.dashed])])
# # Plot contours of Jeans instability
# for MJeans in (0.0, 1.0):
# g.plot(data.function("y(x) = 0.491 + 0.6667*MJeans + 0.333*(x-3.0)",
# context=locals()),
# [line([linestyle.solid, linewidth.Thick])])
# Plot contours of equilibrium T
execdir = os.path.dirname(sys.argv[0])
for col, Av, D in [
[myblue, 0.0, 0.2],
[mygreen, 3.0, 0.2],
cval = c[nx * nlen + mx, ny * nlen + my]
data.append((cval.real, cval.imag, partialdata[mx, my]))
procdict[(nx, ny)] = procid
procids = set(procdict.values())
colors = [
color.hsb(n / (len(procids) - 1) * 0.67, 1, 1) for n in range(len(procids))
]
proccolors = dict(zip(procids, colors))
text.set(text.LatexRunner)
text.preamble(r'\usepackage{arev}\usepackage[T1]{fontenc}')
g = graph.graphxy(width=8,
height=8,
x=graph.axis.lin(title=r'$\mathrm{Re}(c)$'),
y=graph.axis.lin(title=r'$\mathrm{Im}(c)$'))
g.plot(graph.data.points(data, x=1, y=2, color=3),
[graph.style.density(keygraph=None)])
dx = (xmax - xmin) / n
dy = (ymax - ymin) / n
for k, v in procdict.items():
nx, ny = k
tilecolor = proccolors[v]
xll, yll = g.pos(xmin + dx * nx, ymin + dy * ny)
xur, yur = g.pos(xmin + dx * (nx + 1), ymin + dy * (ny + 1))
g.fill(path.rect(xll, yll, xur - xll, yur - yll),
[deco.stroked([color.grey(0)]), tilecolor,
color.transparency(0.5)])
g.writePDFfile()
# convert to PNG with Gimp to keep transparency
