def framebox(nx,
ny,
framecolor,
nw=1,
nh=1,
boxsize=1,
framefactor=0.1,
reducedsize=False):
'''draw color frame in one or across several boxes
The drawing is done on the global canvas called c.
nx, ny: coordinates of lower left corner in number of boxes
framecolor: color
nw, nh: width and height of frame in boxes
framefactor: framewidth as fraction of boxsize
boxsize: side length of fox
reducedsize: if True, the size of the frame is reduced by the framewidth
'''
x = nx * boxsize
y = ny * boxsize
w = nw * boxsize
h = nh * boxsize
if reducedsize:
outer_offset = framefactor * boxsize
inner_offset = 2 * outer_offset
else:
outer_offset = 0
inner_offset = framefactor * boxsize
p = (path.rect(x + outer_offset, y + outer_offset, w - 2 * outer_offset,
h - 2 * outer_offset) +
path.rect(x + inner_offset, y + inner_offset, w - 2 * inner_offset,
h - 2 * inner_offset).reversed())
c.fill(p, [framecolor])
def framebox(nx, ny, framecolor, nw=1, nh=1, boxsize=1, framefactor=0.1,
reducedsize=False):
'''draw color frame in one or across several boxes
The drawing is done on the global canvas called c.
nx, ny: coordinates of lower left corner in number of boxes
framecolor: color
nw, nh: width and height of frame in boxes
framefactor: framewidth as fraction of boxsize
boxsize: side length of fox
reducedsize: if True, the size of the frame is reduced by the framewidth
'''
x = nx*boxsize
y = ny*boxsize
w = nw*boxsize
h = nh*boxsize
if reducedsize:
outer_offset = framefactor*boxsize
inner_offset = 2*outer_offset
else:
outer_offset = 0
inner_offset = framefactor*boxsize
p = (path.rect(x+outer_offset, y+outer_offset,
w-2*outer_offset, h-2*outer_offset)
+ path.rect(x+inner_offset, y+inner_offset,
w-2*inner_offset, h-2*inner_offset).reversed()
)
c.fill(p, [framecolor])
def plot_dataset_ranges(data, width, spacer):
methods = data.keys()
binsizes = numpy.unique(data[methods[0]]['binsize'])
plot_width = width - 0.4
plot_height = plot_width + 0.2
c = canvas.canvas()
for i, binsize in enumerate(binsizes):
img = plot_single_range(data, binsize, plot_width, plot_height)
c.insert(img, [
trafo.translate(
(plot_width + spacer) * i + 0.4, 0.4 + spacer * 0.5)
])
c.text(
0, plot_height * 0.5 + 0.2 + spacer * 0.75, "Dataset correlation",
[text.halign.center, text.valign.top,
text.size(-3),
trafo.rotate(90)])
c.text(plot_width * 2 + spacer * 1.5 + 0.4, 0.35, "Interaction range (bp)",
[text.halign.center, text.valign.bottom,
text.size(-3)])
c.fill(path.rect(0.4, 0.025, 0.2, 0.2), [color.rgb.black])
c.text(0.7, 0.125, "HiFive-Express using raw reads",
[text.halign.left, text.valign.middle,
text.size(-2)])
c.fill(path.rect(plot_width * 2 + spacer * 1.5, 0.025, 0.2, 0.2),
[color.rgb.red])
c.text(plot_width * 2 + spacer * 1.5 + 0.3, 0.125,
"HiFive-Express using distance-corrected reads",
[text.halign.left, text.valign.middle,
text.size(-2)])
return c, plot_height + 0.4 + spacer
def make_picture_for_two_vertices():
c = canvas.canvas()
c.stroke(path.rect(0, 0, 12, 1))
c.stroke(path.rect(1, 0, 1, 1), [style.linewidth.THICK])
c.stroke(path.rect(5, 0, 1, 1), [style.linewidth.THICK])
c.stroke(path.rect(7, 0, 1, 1), [style.linewidth.THICK])
c.stroke(path.rect(10, 0, 1, 1), [style.linewidth.THICK])
c.stroke(path.line(-0.5, 0.5, -0.5, 6), [deco.earrow(size=0.2)])
c.stroke(path.line(1.5, 0.5, 1.5, 5), [deco.earrow(size=0.2)])
c.stroke(path.line(5.5, 0.5, 5.5, 4), [deco.earrow(size=0.2)])
c.stroke(path.line(7.5, 0.5, 7.5, 3), [deco.earrow(size=0.2)])
c.stroke(path.line(10.5, 0.5, 10.5, 2), [deco.earrow(size=0.2)])
c.stroke(path.line(12.5, 0.5, 12.5, 1), [deco.earrow(size=0.2)])
c.stroke(path.line(5.5, 4, 8, 4), [style.linewidth.THIN])
c.stroke(path.line(7, 3, 8, 3), [style.linewidth.THIN])
c.text(7.5, 3.5, r"$\delta_i = l_i - l_{i + 1}$", [text.halign.boxcenter, text.valign.middle])
c.stroke(path.line(6, 0, 6, -1), [style.linewidth.THIN])
c.stroke(path.line(7, 0, 7, -1), [style.linewidth.THIN])
c.text(6.5, -0.4, r"$d_i$", [text.halign.boxcenter, text.valign.middle])
c.text(-0.5, 3, r"$l_0 = 1.0$", [text.halign.boxleft])
c.text(5.5, 2.5, r"$l_i$", [text.halign.boxright])
c.text(7.5, 2, r"$l_{i+1}$", [text.halign.boxleft])
c.text(12.5, 1.1, r"$l_{E+1} = 0.0$", [text.halign.boxcenter])
c.writePDFfile("test_picture.pdf")
def markbox(x, y, boxcolor, linewidthfactor=0.1, boxsize=1):
'''mark box by a colored line
the drawing is done on the global canvas called c
'''
linewidth = linewidthfactor*boxsize
p = (path.rect(x, y, boxsize, boxsize)
+ path.rect(x+linewidth, y+linewidth,
boxsize-2*linewidth, boxsize-2*linewidth).reversed()
)
c.fill(p, [boxcolor])
def draw(dx=0., dy=0., use_arrows=True):
r = 4.*m
syndrome1 = syndrome.copy()
lines = []
for tree in trees:
for p0 in tree.sites:
x0, y0 = coord(*p0)
c.fill(path.circle(x0+dx, y0+dy, r), [grey])
p1 = tree.parent[p0]
#print p0, p1
if p1 is None:
continue # root
lines.append((p0, p1))
x1, y1 = coord(*p1)
#syndrome1[p0] = 0
#c.stroke(path.line(x0+dx, y0+dy, x1+dx, y1+dy),
# [style.linewidth.Thick, deco.earrow(size=0.3)])
if x0==x1:
c.fill(path.rect(x0-r+dx, y0+dy, 2*r, y1-y0), [grey])
else:
c.fill(path.rect(x0+dx, y0-r+dy, x1-x0, 2*r), [grey])
c.fill(path.circle(x0+dx, y0+dy, r), [grey])
c.fill(path.circle(x1+dx, y1+dy, r), [grey])
#c.stroke(path.line(x0+dx, y0+dy, x1+dx, y1+dy),
# [style.linewidth.THICK, style.linecap.round, grey])
if use_arrows:
t = 0.1
s = 1.-t
for (p0, p1) in lines:
x0, y0 = coord(*p0)
x1, y1 = coord(*p1)
#x0, x1 = s*x0+t*x1, s*x1+t*x0
#y0, y1 = s*y0+t*y1, s*y1+t*y0
if syndrome[p1]:
x1 = s*x1+t*x0
y1 = s*y1+t*y0
syndrome1[p0] = 0
c.stroke(path.line(x0+dx, y0+dy, x1+dx, y1+dy),
[style.linewidth.Thick, style.linecap.round, deco.earrow(size=0.2)])
for i, j in sites:
c.stroke(path.rect(j*w+dx, i*h+dy, w-2*m, h-2*m))
if syndrome[i,j]:
x, y = coord(i, j)
anyon(x+dx, y+dy, 0.1*w)
syndrome[:] = syndrome1
def array(shape):
baseshape = (3, 4)
bgcolor = color.grey(0.5)
c = canvas.canvas()
c.text(baseshape[1] / 2, baseshape[0] + 0.3, 'shape=%s' % repr(shape),
[text.halign.center])
if len(shape) == 1:
shape = (1, shape[0])
assert len(shape) == 2
c.stroke(path.rect(0, 0, baseshape[1], baseshape[0]), [bgcolor])
for nx in range(1, baseshape[1]):
c.stroke(path.line(nx, 0, nx, baseshape[0]), [bgcolor])
for ny in range(1, baseshape[0]):
c.stroke(path.line(0, ny, baseshape[1], ny), [bgcolor])
if not (shape == baseshape):
c.fill(path.rect(0, baseshape[0], shape[1], -shape[0]),
[color.rgb(1, 0.8, 0.4)])
if shape[0] in (1, baseshape[0]) and shape[1] in (1, baseshape[1]):
for nx in range(baseshape[1]):
for ny in range(baseshape[0]):
c.text(
nx + 0.5, baseshape[0] - ny - 0.5,
str(baseshape[1] * min(ny, shape[0] - 1) +
min(nx, shape[1] - 1) + 1),
[text.halign.center, text.valign.middle, bgcolor])
else:
alertcolor = color.rgb(0.6, 0, 0)
c.stroke(path.line(0, 0, baseshape[1], baseshape[0]),
[alertcolor, style.linewidth.Thick])
c.stroke(path.line(0, baseshape[0], baseshape[1], 0),
[alertcolor, style.linewidth.Thick])
else:
for nx in range(baseshape[1]):
for ny in range(baseshape[0]):
c.text(nx + 0.5, baseshape[0] - ny - 0.5,
str(baseshape[1] * ny + nx + 1),
[text.halign.center, text.valign.middle])
c.stroke(path.rect(0, baseshape[0], shape[1], -shape[0]))
for nx in range(1, shape[1]):
c.stroke(path.line(nx, baseshape[0], nx, baseshape[0] - shape[0]))
for ny in range(1, shape[0]):
c.stroke(path.line(0, ny, shape[1], ny))
if not (shape == baseshape):
for nx in range(shape[1]):
for ny in range(shape[0]):
c.text(nx + 0.5, baseshape[0] - ny - 0.5,
str(baseshape[1] * ny + nx + 1),
[text.halign.center, text.valign.middle])
return c
def arraygraphics(a,
idxstr,
title=True,
xscale=1.0,
fgcolor=color.grey(1),
bgcolor=color.hsb(0.9, 1, 0.5)):
"""create a graphical representation of a two-dimensional array
a array containing the data to be shown
slicestr string defining the slice to be highlighted
xscale PyX scaling for text
fgcolor color of highlighted data
bgcolor color of highlighted cells
"""
assert a.ndim == 2
n0, n1 = a.shape
highlighted = np.zeros_like(a, dtype=bool)
exec("highlighted{} = True".format(idxstr))
unit.set(xscale=xscale)
text.set(text.LatexRunner)
text.preamble(
r'\usepackage[sfdefault,scaled=.85,lining]{FiraSans}\usepackage{newtxsf}'
)
c = canvas.canvas()
for ny, nx in zip(*np.nonzero(highlighted)):
c.fill(path.rect(nx, n0 - ny, 1, -1), [bgcolor])
c.stroke(path.rect(0, 0, n1, n0))
for nx in range(1, n1):
c.stroke(path.line(nx, 0, nx, n0))
for ny in range(1, n0):
c.stroke(path.line(0, ny, n1, ny))
textcentered = [text.halign.center, text.valign.middle]
textcentered_highlighted = textcentered + [fgcolor]
for nx in range(n1):
for ny in range(n0):
if highlighted[ny, nx]:
textattrs = textcentered_highlighted
else:
textattrs = textcentered
c.text(nx + 0.5, n0 - ny - 0.5, a[ny, nx], textattrs)
if title:
textcolor = bgcolor
else:
textcolor = color.grey(1)
titlestr = r"\Large a" + idxstr.replace('%', '\%')
c.text(0.5 * n1, n0 + 0.4, titlestr, [text.halign.center, textcolor])
return c
def rectangular_band(g, x_coord_init, y_coord_init, x_coord_final,
y_coord_final, band_color):
"""
Function that draws a rectangular band around the given coordinates
INPUTS:
g (Object) A graph-type object to which you want to add the text
x_coord_init (Double) x-coordinate (in plot units) at which you want the band
to start.
y_coord_init (Double) y-coordinate (in plot units) at which you want the band
to start.
x_coord_final (Double) x-coordinate (in plot units) at which you want the band
to end.
y_coord_final (Double) y-coordinate (in plot units) at which you want the band
to end.
band_color (instance) Instance color that defines the color of the band.
"""
x0, y0 = g.pos(x_coord_init, y_coord_init)
xf, yf = g.pos(x_coord_final, y_coord_final)
x = x0
y = y0
w = np.abs(x0 - xf)
h = np.abs(y0 - yf)
g.fill(pyx_path.rect(x, y, w, h), [band_color])
def array34(arange, hlshape=None):
c = canvas.canvas()
if hlshape is None:
c.text(2, 3.3, 'shape=(3, 4)', [text.halign.center])
else:
c.text(2, 3.3, 'shape=%s' % repr(hlshape), [text.halign.center])
if hlshape is not None:
if len(hlshape) == 1:
hlshape = (1, hlshape[0])
if arange:
gridcolor = color.grey(0)
else:
gridcolor = color.grey(0.5)
if hlshape is None:
arange = True
elif (hlshape[0] in (1, 3)) and (hlshape[1] in (1, 4)):
arange = False
else:
arange = None
drawgrid(c, 4, 3, 0, gridcolor, arange=arange)
if hlshape is not None:
c.stroke(path.rect(0, 3, hlshape[1], -hlshape[0]),
[deco.filled([color.rgb(1, 0.8, 0.4)])])
drawgrid(c, hlshape[1], hlshape[0], 3-hlshape[0], arange=False)
if arange is None:
alertcolor = color.rgb(0.6, 0, 0)
c.stroke(path.line(0, 0, 4, 3), [alertcolor, style.linewidth.Thick])
c.stroke(path.line(0, 3, 4, 0), [alertcolor, style.linewidth.Thick])
return c
def makebinaries(number, y0):
size = 0.4
dist = 0.1
for n in range(32):
c.stroke(path.rect(n * size + (n / 8) * dist, y0, size, size))
c.text((n + 0.5) * size + (n / 8) * dist, y0 + 0.07,
r"\sffamily %i" % ((number >> 31 - n) & 1),
[text.halign.center])
if number >> 31:
c.text(32.2 * size + 5 * dist, y0 + 0.07,
r"\sffamily = -%i" % ((number ^ 0xffffffff) + 1))
else:
c.text(32.2 * size + 5 * dist, y0 + 0.07, r"\sffamily = %i" % number)
p = path.path(path.moveto(0.2 * size, size + 0.03),
path.lineto(0.2 * size, size + 0.07),
path.lineto(3.8 * size, size + 0.07),
path.lineto(3.8 * size, size + 0.03))
for n in range(4):
c.stroke(p, [trafo.translate(n * (8 * size + dist), y0)])
c.text(n * (8 * size + dist) + 2 * size, size + 0.14 + y0,
r"\sffamily %X" % ((number >> ((3 - n) * 8 + 4)) & 15),
[text.halign.center])
c.stroke(p, [trafo.translate(n * (8 * size + dist) + 4 * size, y0)])
c.text(n * (8 * size + dist) + 6 * size, size + 0.14 + y0,
r"\sffamily %X" % ((number >>
((3 - n) * 8)) & 15), [text.halign.center])
def draw_config(name):
c = canvas.canvas()
config = configs[name]
ysize = len(config)
xsize = len(config[0])
for nx in range(xsize):
for ny in range(ysize):
if config[ny][nx]:
c.fill(path.rect(nx, ysize-ny, 1, -1))
strokecolor = color.grey(0.6)
c.stroke(path.rect(0, 0, xsize, ysize), [strokecolor])
for nx in range(1, xsize):
c.stroke(path.line(nx, 0, nx, ysize), [strokecolor])
for ny in range(1, ysize):
c.stroke(path.line(0, ny, xsize, ny), [strokecolor])
return c
def makebinaries(number, y0):
size = 0.4
dist = 0.1
for n in range(32):
c.stroke(path.rect(n*size+(n/8)*dist, y0, size, size))
c.text((n+0.5)*size+(n/8)*dist, y0+0.07,
r"\sffamily %i" % ((number >> 31-n) & 1),
[text.halign.center])
if number >> 31:
c.text(32.2*size+5*dist, y0+0.07,
r"\sffamily = -%i" % ((number ^ 0xffffffff)+1))
else:
c.text(32.2*size+5*dist, y0+0.07, r"\sffamily = %i" % number)
p = path.path(path.moveto(0.2*size, size+0.03),
path.lineto(0.2*size, size+0.07),
path.lineto(3.8*size, size+0.07),
path.lineto(3.8*size, size+0.03))
for n in range(4):
c.stroke(p, [trafo.translate(n*(8*size+dist), y0)])
c.text(n*(8*size+dist)+2*size, size+0.14+y0,
r"\sffamily %X" % ((number >> ((3-n)*8+4)) & 15),
[text.halign.center])
c.stroke(p, [trafo.translate(n*(8*size+dist)+4*size, y0)])
c.text(n*(8*size+dist)+6*size, size+0.14+y0,
r"\sffamily %X" % ((number >> ((3-n)*8)) & 15),
[text.halign.center])
def draw_points_lines_crs(points: torch.Tensor,
lines: torch.Tensor,
crs: torch.Tensor,
filename,
size=1,
lw=1,
clw=1,
pcols=None,
lcols=None,
crscols=None,
canvas_clip=None,
svg=False):
if canvas_clip is not None:
c = canvas.canvas([canvas.clip(path.rect(*canvas_clip))])
else:
c = canvas.canvas()
draw_points_to_canvas(c, points, size, pcols)
draw_lines_to_canvas(c, lines, lw, lcols)
draw_crs_to_canvas(c, crs, clw, crscols)
if svg:
c.writeSVGfile(file=filename)
else:
c.writePDFfile(file=filename)
def guide_layer(holes):
guide_size = 1.2
# Get guide fiber information
iguide = np.nonzero(np.array(holes['holetype']) == b'GUIDE')[0]
guide_xfocal = np.array(holes['xfocal'])[iguide]
guide_yfocal = np.array(holes['yfocal'])[iguide]
guidenum = np.array(holes['iguide'])[iguide]
# Set up object to print
clippath = path.circle(0., 0., interior_radius)
clipobject = canvas.clip(clippath)
interior = canvas.canvas([clipobject])
for indx in range(len(guide_xfocal)):
interior.stroke(
path.rect((guide_yfocal[indx] / 10.) - guide_size * 0.5,
(guide_xfocal[indx] / 10.) - guide_size * 0.5,
guide_size, guide_size),
[style.linewidth.THick, color.cmyk.Black])
interior.text(
(guide_yfocal[indx] / 10.) + guide_size * 0.66,
(guide_xfocal[indx] / 10.),
r"\font\myfont=cmr10 at 35pt {\myfont " + str(guidenum[indx]) +
"}", [text.halign.boxleft, text.valign.middle, text.size.Huge])
return interior
def state(x0, y0, r, c):
x1 = x0 - r / sqrt(2)
y1 = y0 + r / sqrt(2)
x2 = x0 - 3 * r / 4 / sqrt(2)
y2 = y1 + r / 8
x3 = x0 - r / 4 / sqrt(2)
y3 = y1 - r / 8
x4 = x0 + r / 4 / sqrt(2)
y4 = y1 + r / 8
x5 = x0 + 3 * r / 4 / sqrt(2)
y5 = y1 - r / 8
x6 = x0 + r / sqrt(2)
y6 = y1
delta = r / 40
c.fill(path.circle(x0, y0, r), [color.cmyk.RoyalBlue])
c.fill(path.rect(x1 + delta, y0 + delta,
r * sqrt(2) - 2 * delta, r), [color.rgb.white])
inside = path.curve(x1, y1, x2, y2, x3, y3, x0, y1) << \
path.curve(x0, y1, x4, y4, x5, y5, x6, y6) << \
path.line(x6, y6, x6, y0) << \
path.line(x6, y0, x1, y0)
inside.append(path.closepath())
c.fill(inside, [color.cmyk.RoyalBlue])
c.stroke(path.circle(x0, y0, r), [style.linewidth(r / 25)])
def array34(arange, hlshape=None):
c = canvas.canvas()
if hlshape is None:
c.text(2, 3.3, 'shape=(3, 4)', [text.halign.center])
else:
c.text(2, 3.3, 'shape=%s' % repr(hlshape), [text.halign.center])
if hlshape is not None:
if len(hlshape) == 1:
hlshape = (1, hlshape[0])
if arange:
gridcolor = color.grey(0)
else:
gridcolor = color.grey(0.5)
if hlshape is None:
arange = True
elif (hlshape[0] in (1, 3)) and (hlshape[1] in (1, 4)):
arange = False
else:
arange = None
drawgrid(c, 4, 3, 0, gridcolor, arange=arange)
if hlshape is not None:
c.stroke(path.rect(0, 3, hlshape[1], -hlshape[0]),
[deco.filled([color.rgb(1, 0.8, 0.4)])])
drawgrid(c, hlshape[1], hlshape[0], 3 - hlshape[0], arange=False)
if arange is None:
alertcolor = color.rgb(0.6, 0, 0)
c.stroke(path.line(0, 0, 4, 3), [alertcolor, style.linewidth.Thick])
c.stroke(path.line(0, 3, 4, 0), [alertcolor, style.linewidth.Thick])
return c
def plot_key(width, height):
c = canvas.canvas()
step = height / float(len(method_colors))
for i, meth in enumerate(['HiFive-Probability', 'HiFive-Express', 'HiFive-Binning']):
c.fill(path.rect(0.2, height - step * (i + 0.5) - 0.1, 0.2, 0.2),
[method_colors[meth]])
c.text(0.5, height - step * (i + 0.5), meth, [text.halign.left, text.valign.middle, text.size(-2)])
return c
def plot_key(width, height):
c = canvas.canvas()
w = height / 7.0
for i, meth in enumerate(methods):
c.fill(path.rect(1.0, (6 - i) * w - 0.1, 0.2, 0.2), [method_colors[meth]])
c.text(1.3, (6 - i) * w, "%s" % meth_names[meth],
[text.halign.left, text.valign.middle, text.size(-3)])
return c
def rect(x, y, dx, dy, intxt=None, bottxt=None):
"x, y: lower left"
c.stroke(path.rect(x, y, dx, dy), [style.linestyle.dashed, style.linewidth.thick, green])
if intxt:
c.text(x+dx/2., y+dy/2., intxt,
[text.valign.middle, text.halign.boxcenter])
if bottxt:
c.text(x+dx-pip, y-pip, bottxt,
[text.valign.top, text.halign.boxright])
def plot_key(width, height):
c = canvas.canvas()
w = height / 7.0
for i, meth in enumerate(methods):
c.fill(path.rect(1.0, (6 - i) * w - 0.1, 0.2, 0.2),
[method_colors[meth]])
c.text(1.3, (6 - i) * w, "%s" % meth_names[meth],
[text.halign.left, text.valign.middle,
text.size(-3)])
return c
def plot_dataset_ranges(data, width, spacer):
methods = data.keys()
binsizes = numpy.unique(data[methods[0]]['binsize'])
plot_width = width - 0.4
plot_height = plot_width + 0.2
c = canvas.canvas()
for i, binsize in enumerate(binsizes):
img = plot_single_range(data, binsize, plot_width, plot_height)
c.insert(img, [trafo.translate((plot_width + spacer) * i + 0.4, 0.4 + spacer * 0.5)])
c.text(0, plot_height * 0.5 + 0.2 + spacer * 0.75, "Dataset correlation",
[text.halign.center, text.valign.top, text.size(-3), trafo.rotate(90)])
c.text(plot_width * 2 + spacer * 1.5 + 0.4, 0.35, "Interaction range (bp)",
[text.halign.center, text.valign.bottom, text.size(-3)])
c.fill(path.rect(0.4, 0.025, 0.2, 0.2), [color.rgb.black])
c.text(0.7, 0.125, "HiFive-Express using raw reads", [text.halign.left, text.valign.middle, text.size(-2)])
c.fill(path.rect(plot_width * 2 + spacer * 1.5, 0.025, 0.2, 0.2), [color.rgb.red])
c.text(plot_width * 2 + spacer * 1.5 + 0.3, 0.125, "HiFive-Express using distance-corrected reads",
[text.halign.left, text.valign.middle, text.size(-2)])
return c, plot_height + 0.4 + spacer
def draw(dx=0., dy=0.):
r = 4.*m
data1 = data.copy()
lines = []
for tree in trees:
for p0 in tree.sites:
x0, y0 = coord(*p0)
c.fill(path.circle(x0+dx, y0+dy, r), [grey])
p1 = tree.parent[p0]
#print p0, p1
if p1 is None:
continue # root
lines.append((p0, p1))
x1, y1 = coord(*p1)
#data1[p0] = 0
#c.stroke(path.line(x0+dx, y0+dy, x1+dx, y1+dy),
# [style.linewidth.Thick, deco.earrow(size=0.3)])
if x0==x1:
c.fill(path.rect(x0-r+dx, y0+dy, 2*r, y1-y0), [grey])
else:
c.fill(path.rect(x0+dx, y0-r+dy, x1-x0, 2*r), [grey])
c.fill(path.circle(x0+dx, y0+dy, r), [grey])
c.fill(path.circle(x1+dx, y1+dy, r), [grey])
#c.stroke(path.line(x0+dx, y0+dy, x1+dx, y1+dy),
# [style.linewidth.THICK, style.linecap.round, grey])
for (p0, p1) in lines:
x0, y0 = coord(*p0)
x1, y1 = coord(*p1)
data1[p0] = 0
c.stroke(path.line(x0+dx, y0+dy, x1+dx, y1+dy),
[style.linewidth.Thick, deco.earrow(size=0.3)])
for i, j in sites:
c.stroke(path.rect(j*w+dx, i*h+dy, w-2*m, h-2*m))
if data[i,j]:
x, y = coord(i, j)
anyon(x+dx, y+dy, 0.1*w)
data[:] = data1
def plot_key(width, height, data):
methods = data.keys()
methods.sort()
c = canvas.canvas()
step = height / float(len(method_colors))
for i, meth in enumerate(methods):
c.fill(path.rect(0.2, height - step * (i + 0.5) - 0.1, 0.2, 0.2),
[method_colors[meth]])
c.text(0.5, height - step * (i + 0.5), meth, [text.halign.left, text.valign.middle, text.size(-2)])
return c
def manifold(x, y, labels, count):
if count in [0, 2]:
c.stroke(path.line(x-r0, y, x+r1+r0, y), st_curve)
else:
extra = list(st_curve)
#if count==3:
# extra.append(trafo.scale(x=x, y=y, sx=1, sy=-1))
Turtle(x-0.85*r0, y, pi/2).\
fwd(0.3).\
right(0.25*pi, 0.4).left(0.50*pi, 0.73).left(0.88*pi, 0.15).\
fwd(0.55).\
right(0.88*pi, 0.15).right(0.50*pi, 0.73).\
left(0.25*pi, 0.52).goto(x+r1+r0, y).\
stroke(extra)
if count==0:
c.text(x+r1+r0, y-0.2, "$f$", northwest)
else:
c.text(x+r1+r0, y-0.2, "$R^{a_1a_2}_{b_1}f$", northwest)
c.text(x+(r0+r1)/2, y+0.7, "$f'$", southwest)
if count == 0:
Turtle(x, y, 3*pi/4).left(0.95*pi/2, 2**0.5/2*r1).stroke(st_target+[trafo.scale(x=x, y=y, sx=1, sy=-1)])
elif count == 3:
Turtle(x-0.05, y, 0.90*pi).left(0.30*pi, 0.8).left(0.3*pi, 2.8).\
stroke(st_target+[trafo.scale(x=x, y=y, sx=1, sy=-1)])
else:
Turtle(x+r0, y, 3*pi/4).left(0.95*pi/2, 2**0.5/2*(r1-r0)).stroke(st_target)
for i in range(3):
_x = [x, x+r0, x+r1][i]
p = path.circle(_x, y, 0.08)
c.fill(p, [white])
c.stroke(p)
ydelta = -0.25
xdelta = 0.00
if count==3 and labels[i]=="a_2":
ydelta = -0.35
xdelta = +0.1
if count==3 and labels[i]=="a_1":
xdelta = -0.1
ydelta = +0.3
c.text(_x+xdelta, y+ydelta, r"$\scriptstyle %s$"%labels[i], center)
x1 = x+(r0+r1)/2.
c.text(x1, y-0.2, "...", north)
c.fill(path.rect(x1-0.4, y-0.1, 0.8, 0.2), [white])
c.stroke(path.line(x1-0.4, y, x1+0.4, y), [green, style.linewidth.THick]+st_dotted)
c.stroke(path.circle(x+r0/2, y, r0), [trafo.scale(x=x+r0/2, y=y, sx=1.0, sy=0.8)])
c.text(x, y+0.3*h, "$b_1$", southeast)
def arraygraphics(a, idxstr, title=True, xscale=1.0,
fgcolor=color.grey(1), bgcolor=color.hsb(0.9, 1, 0.5)):
"""create a graphical representation of a two-dimensional array
a array containing the data to be shown
slicestr string defining the slice to be highlighted
xscale PyX scaling for text
fgcolor color of highlighted data
bgcolor color of highlighted cells
"""
assert a.ndim == 2
n0, n1 = a.shape
highlighted = np.zeros_like(a, dtype=bool)
exec("highlighted{} = True".format(idxstr))
unit.set(xscale=xscale)
text.set(text.LatexRunner)
text.preamble(r'\usepackage[sfdefault,scaled=.85,lining]{FiraSans}\usepackage{newtxsf}')
c = canvas.canvas()
for ny, nx in zip(*np.nonzero(highlighted)):
c.fill(path.rect(nx, n0-ny, 1, -1), [bgcolor])
c.stroke(path.rect(0, 0, n1, n0))
for nx in range(1, n1):
c.stroke(path.line(nx, 0, nx, n0))
for ny in range(1, n0):
c.stroke(path.line(0, ny, n1, ny))
textcentered = [text.halign.center, text.valign.middle]
textcentered_highlighted = textcentered+[fgcolor]
for nx in range(n1):
for ny in range(n0):
if highlighted[ny, nx]:
textattrs = textcentered_highlighted
else:
textattrs = textcentered
c.text(nx+0.5, n0-ny-0.5, a[ny, nx], textattrs)
if title:
textcolor = bgcolor
else:
textcolor = color.grey(1)
titlestr = r"\Large a"+idxstr.replace('%', '\%')
c.text(0.5*n1, n0+0.4, titlestr, [text.halign.center, textcolor])
return c
def plot_key(width, height):
c = canvas.canvas()
step = height / float(len(method_colors))
for i, meth in enumerate(
['HiFive-Probability', 'HiFive-Express', 'HiFive-Binning']):
c.fill(path.rect(0.2, height - step * (i + 0.5) - 0.1, 0.2, 0.2),
[method_colors[meth]])
c.text(0.5, height - step * (i + 0.5), meth,
[text.halign.left, text.valign.middle,
text.size(-2)])
return c
def clear(self):
"""
Erases the contents of this Window
All Turtles and Pens are eliminated from the Window. Any attempt to use a
previously created :class:`Turtle` or :class:`Pen` will fail.
"""
from pyx import canvas
from pyx import path
clippath = path.rect(self.x, self.y, self.width, self.height)
self._canvas = canvas.canvas([canvas.clip(clippath)])
self._turtles = []
self._pencils = []
def file(c, size=1, xoff=0, yoff=0, attrs=[], title=''):
w = 3
h = 2.1
fold = 0.6
outline = path.path(path.moveto(0, 0), path.lineto(w, 0),
path.lineto(w, h - fold), path.lineto(w - fold, h),
path.lineto(0, h), path.closepath())
foldpath = path.path(path.moveto(w - fold, h),
path.lineto(w - fold, h - fold),
path.lineto(w, h - fold))
c1 = canvas.canvas()
c1.stroke(outline, attrs)
d = deformer.smoothed(0.2)
c1.stroke(d.deform(foldpath), attrs)
c1.stroke(path.rect(0.1 * w, 0.3 * h, 0.6 * w, 0.1 * h))
c1.stroke(path.rect(0.1 * w, 0.45 * h, 0.6 * w, 0.1 * h))
c1.stroke(path.rect(0.1 * w, 0.6 * h, 0.6 * w, 0.1 * h))
c1.stroke(path.rect(0.1 * w, 0.75 * h, 0.6 * w, 0.1 * h))
c1.text(0.1, 0.1, r'\sffamily ' + title, [trafo.scale(0.7)])
myattrs = [trafo.translate(xoff, yoff), trafo.scale(size)]
myattrs.extend(attrs)
c.insert(c1, myattrs)
def generate_tile(item):
title = item['title']
print(title)
image = item['image']
if item['quantity'] > 1:
handle_multiple(item)
return
#72dpi is illustrator default
drawing = svgfile.svgfile(0, 0, 'images%s' % image, parsed=True, resolution=72)
setEtch(drawing.canvas)
canvas_size = get_canvas_size(item)
drawing_size = (drawing.bbox().width(), drawing.bbox().height())
dir = 'tiles/%s' % item['type']
if not os.path.exists(dir):
os.makedirs(dir)
c = canvas.canvas()
center = ( (canvas_size[0] - drawing_size[0]) / 2, (canvas_size[1] - drawing_size[1]) / 2 )
c.insert(drawing, [trafo.translate(center[0], center[1])])
yMargin = (canvas_size[1] - drawing_size[1]) / 2
yPos = yMargin - yMargin / 2
baseline = text.parbox.middle
textbox = '{\large %s}' % title
if 'subtitle' in item:
textbox += '\n\n'
textbox += item['subtitle']
if yPos < (unit.t_inch / 2):
baseline = text.parbox.bottom
c.text(canvas_size[0] / 2, yPos, textbox, [
text.halign.boxcenter,
text.halign.flushcenter,
text.parbox(canvas_size[0] - .25 * unit.t_inch, baseline = baseline)
])
#draw Cut line
if CUT_LINE:
c.stroke(
path.rect(0, 0, canvas_size[0], canvas_size[1]),
[ style.linewidth(0.001), color.rgb.red ]
)
p = document.page(c, bbox=bbox.bbox(0, 0, canvas_size[0], canvas_size[1]))
d = document.document([p])
d.writeSVGfile('%s/%s.svg' % (dir, slugify(title)))
def drawgrid(c, nxcells, nycells, yoff, gridcolor=color.grey(0), arange=None):
c.stroke(path.rect(0, yoff, nxcells, nycells), [gridcolor])
for nx in range(nxcells-1):
c.stroke(path.line(nx+1, yoff, nx+1, yoff+nycells), [gridcolor])
for ny in range(nycells-1):
c.stroke(path.line(0, yoff+ny+1, nxcells, yoff+ny+1), [gridcolor])
entry = '1'
if arange is not None:
for nx in range(nxcells):
for ny in range(nycells):
if arange:
entry = str(4*ny+nx)
c.text(nx+0.5, 2.5-ny, entry,
[text.halign.center, text.valign.middle, gridcolor])
def plot_correlation_diffs(corr1, corr2, name, width, height):
ho = 1.2
vo = 0.4
plot_width = width - ho
plot_height = height - vo
diffs = {}
ymin = numpy.inf
ymax = -numpy.inf
for n in ['Phillips', 'Nora']:
for meth in meth_names.keys():
cname = "%s_%s" % (meth, n)
diff = corr2[cname] - corr1[cname]
ymin = min(ymin, diff)
ymax = max(ymax, diff)
for meth in meth_names.keys():
cname = "%s_%s" % (meth, name)
diffs[meth] = corr2[cname] - corr1[cname]
yspan = ymax - ymin
ymin -= yspan * 0.05
ymax += yspan * 0.05
yspan = ymax - ymin
c = canvas.canvas()
g = graph.graphxy(
width=plot_width,
height=plot_height,
x=graph.axis.bar(painter=graph.axis.painter.bar(nameattrs=None)),
y=graph.axis.lin(painter=painter, min=ymin, max=ymax),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(parter=None, min=0, max=1))
w = plot_width / float(len(meth_names) + 1)
y0 = -ymin / yspan * plot_height
for i, meth in enumerate(methods):
col = method_colors[meth]
g.stroke(
path.rect((i + 0.5) * w, y0, w, diffs[meth] / yspan * plot_height),
[deco.filled([col])])
g.stroke(path.line(0, y0, plot_width, y0),
[style.linestyle.dotted, style.linewidth.THin])
c.insert(g, [trafo.translate(ho, vo)])
c.text(
0, plot_height * 0.5 + vo, r"$r_{0K} - r_{50K}$",
[text.halign.center, text.valign.top,
text.size(-3),
trafo.rotate(90)])
c.text(plot_width * 0.5 + ho, vo * 0.5, name,
[text.halign.center, text.valign.middle,
text.size(-3)])
return c
def test_pie(radius, start, end):
c = canvas.canvas()
container = path.rect(-(radius + 1), -(radius + 1), 2 * (radius + 1),
2 * (radius + 1))
c.stroke(container, [style.linewidth(0.001), color.rgb.red])
pie = path.path(path.moveto(0, 0), path.arc(0, 0, radius, start, end),
path.closepath())
c.stroke(pie, [
style.linewidth(0.1),
pyx.color.rgb(1, 1, 1),
deco.filled([color.rgb.red])
])
c.writeSVGfile("figure")
def plot_key(width, height):
c = canvas.canvas()
wstep = width / 2.0
hstep = height / 3
for i in range(5):
x = wstep * (i / 3)
y = height - (i % 3 + 0.5) * hstep
c.fill(path.rect(x + 0.1, y - 0.15, 0.3, 0.3), [step_colors[i]])
temp = step_names[str(i)].split(' ')
if len(temp) > 2:
c.text(x + 0.5, y + 0.13, ' '.join(temp[:2]),
[text.halign.left, text.valign.middle, text.size(-2)])
c.text(x + 0.5, y - 0.13, temp[-1],
[text.halign.left, text.valign.middle, text.size(-2)])
else:
c.text(x + 0.5, y, step_names[str(i)],
[text.halign.left, text.valign.middle, text.size(-2)])
return c
def RectMid(canv,
pt,
w,
h,
fi=0,
linewidth=LINE_DEF_WIDTH,
linecolor=LINE_DEF_COLOR,
fillcolor=None,
mstyle=[]):
rect = path.rect(pt.x, pt.y - h / 2, w, h)
rto = trafo.rotate(fi, pt.x, pt.y)
if fillcolor is not None:
canv.fill(rect, [fillcolor, rto])
canv.stroke(rect, [style.linewidth(linewidth), linecolor, rto] + mstyle)
def plot(self, canvas, shape="s"):
"""Plot this direction on a pyx canvas.
The direction will be transformed onto a Lambert equal-area
projection and plotted as a square, circle, or triangle
(shape parameter: s, c, or t).
"""
(x, y) = self.project()
if shape == "s":
canvas.stroke(path.rect(x - 0.1, y - 0.1, 0.2, 0.2))
elif shape == "t":
s = 0.15
canvas.stroke(path.path(path.moveto(x, y + s),
path.rlineto(-0.866 * s, -1.5 * s),
path.rlineto(2 * .866 * s, 0),
path.closepath()))
elif shape == "c":
canvas.stroke(path.circle(x, y, 0.1))
def generate_diagrams(data, shape_canvas, text_canvas, settings, source_path):
diagrams = {}
# draw bounding box so the file is the right size and shape
x = settings['output']['x']
y = settings['output']['y']
# draw the bounding box
shape_canvas.stroke(
path.rect(-0.25 * x, -0.5 * y, x, y),
[color.rgb.white, style.linewidth(0.001)])
for entry in data:
name = entry[0]
origin = entry[1]
data_source = entry[2]
diagrams[name] = Sunburst(shape_canvas, text_canvas, settings,
source_path, name, origin, data_source)
diagrams[name].draw()
stop_trace()
return diagrams
def make_moon_key(canv, chart) :
large_moon_rad = 0.16
small_moon_rad = 0.12
x = 0.0
y = -1.8
canv.fill(path.rect(x, y, chart.width, 1.0),
[color.rgb(0.0, 0.0, 0.0)])
for i in range(8) :
X = 1.0-(i+1.0)/9.0
canv.fill(waning_moon(X, small_moon_rad, x+(i+4.0)/4.0, -1.3),
[style.linejoin.bevel,mooncolorlight])
canv.text(x+1.8, -1.1,
r'{\footnotesize\sffamily Küçülen Ay}',
[text.halign.center,text.valign.baseline,mooncolorlight])
canv.text(x+1.8, -1.7,
r"{\scriptsize\sffamily (Ay'ın doğuş zamanları)}",
[text.halign.center,text.valign.baseline,mooncolorlight])
for i in range(8) :
X = (i+1.0)/9.0
canv.fill(waxing_moon(X, small_moon_rad, x+(i+4.0)/4.0+3.0, -1.3),
[style.linejoin.bevel,mooncolordark])
canv.text(x+1.8+3.0, -1.1,
r'{\footnotesize\sffamily Büyüyen Ay}',
[text.halign.center,text.valign.baseline,mooncolordark])
canv.text(x+1.8+3.0, -1.7,
r"{\scriptsize\sffamily (Ay'ın batış zamanları)}",
[text.halign.center,text.valign.baseline,mooncolordark])
# new moon, first quarter
# full moon, last quarter
canv.stroke(path.circle(x+8.5,-1.1,large_moon_rad),[mooncolorlight,pyx.deco.filled([mooncolordark])])
canv.text(x+8.25, -1.2, r'{\footnotesize\sffamily Yeni ay}',
[text.halign.right,text.valign.baseline, mooncolordark])
canv.stroke(first_quarter_moon(large_moon_rad, x+8.9,-1.1),[mooncolordark,pyx.deco.filled([mooncolordark])])
canv.text(x+9.25, -1.2, r'{\footnotesize\sffamily İlk dördün}',
[text.halign.left,text.valign.baseline, mooncolordark])
canv.stroke(path.circle(x+8.5,-1.5,large_moon_rad),[mooncolorlight,pyx.deco.filled([mooncolorlight])])
canv.text(x+8.25, -1.6, r'{\footnotesize\sffamily Dolunay}',
[text.halign.right,text.valign.baseline, mooncolorlight])
canv.stroke(last_quarter_moon(large_moon_rad, x+8.9,-1.5),[mooncolorlight,pyx.deco.filled([mooncolorlight])])
canv.text(x+9.25, -1.6, r'{\footnotesize\sffamily Son dördün}',
[text.halign.left,text.valign.baseline, mooncolorlight])
def whiteout_layer(holes):
whiteout = canvas.canvas()
for indx in range(len(holes['xfocal'])):
radius = 0.25
if (holes['holetype'][indx] == b'GUIDE'):
radius = 0.54
if (holes['holetype'][indx] == b'ALIGNMENT'):
radius = 0.1
if (holes['holetype'][indx] == b'MANGA'):
radius = 0.4
if (holes['holetype'][indx] == b'MANGA_SINGLE'):
radius = 0.4
if (holes['holetype'][indx] == b'MANGA_ALIGNMENT'):
radius = 0.2
if (holes['holetype'][indx] == b'CENTER'):
radius = 0.36
if (holes['holetype'][indx] == b'TRAP'):
radius = 0.45
if (holes['holetype'][indx] == b'ACQUISITION_CENTER'):
radius = 2.9
whiteout.fill(
path.circle(holes['yfocal'][indx] / 10.,
holes['xfocal'][indx] / 10., radius),
[color.rgb.white])
ioffaxis = np.nonzero(
np.array(holes['holetype']) == b'ACQUISITION_OFFAXIS')[0]
if (len(ioffaxis) == 0):
return whiteout
if (len(ioffaxis) > 1):
print("Expect just one off-axis acquisition camera.")
sys.exit()
offaxis_xfocal = np.array(holes['xfocal'])[ioffaxis[0]]
offaxis_yfocal = np.array(holes['yfocal'])[ioffaxis[0]]
whiteout.fill(
path.rect((offaxis_yfocal / 10.) - offaxis_ysize * 0.49,
(offaxis_xfocal / 10.) - offaxis_xsize * 0.49,
0.98 * offaxis_ysize, 0.98 * offaxis_xsize),
[color.rgb.white])
return whiteout
def plot_key(width, height):
c = canvas.canvas()
wstep = width / 2.0
hstep = height / 3
for i in range(5):
x = wstep * (i / 3)
y = height - (i % 3 + 0.5) * hstep
c.fill(path.rect(x + 0.1, y - 0.15, 0.3, 0.3), [step_colors[i]])
temp = step_names[str(i)].split(' ')
if len(temp) > 2:
c.text(x + 0.5, y + 0.13, ' '.join(temp[:2]),
[text.halign.left, text.valign.middle,
text.size(-2)])
c.text(x + 0.5, y - 0.13, temp[-1],
[text.halign.left, text.valign.middle,
text.size(-2)])
else:
c.text(x + 0.5, y, step_names[str(i)],
[text.halign.left, text.valign.middle,
text.size(-2)])
return c
def flush(self):
"""
Writes out all of the pens and turtles attached to the window.
"""
# Draw a bounding box
from pyx import path
from pyx import text
r = path.rect(0, 0, self.width, self.height)
self._canvas.stroke(r)
for t in self._turtles:
t.flush()
for p in self._pencils:
p.flush()
# Write the title, if we have one
if not self.title is None:
self._canvas.text(
0, self.height / 2.0 - 30, "{\\Huge %s}" % self.title,
[text.halign.boxcenter, self._offset()])
def plot_bar(data, ranges, height, scale, split):
c = canvas.canvas()
pos = 0.0
x1 = 0.0
for i in range(5):
if str(i) in data:
x2 = data[str(i)] / 60.0 + pos
pos2 = x2
for j in range(1, ranges.shape[0]):
if x2 > ranges[j, 0] and x2 < ranges[j, 1]:
for k in range(j):
x2 -= ranges[k + 1, 0] - ranges[k, 1]
break
c.fill(path.rect(x1 * scale, 0, (x2 - x1) * scale, height), [step_colors[i]])
split_pos = ranges[0, 1] * scale
for j in range(ranges.shape[0] - 1):
if pos2 > ranges[j, 1]:
c.insert(split, [trafo.translate(split_pos, height * 0.5)])
split_pos += (ranges[j + 1, 1] - ranges[j + 1, 0]) * scale
pos += data[str(i)] / 60.0
x1 = x2
return c
def plot_correlation_diffs(corr1, corr2, name, width, height):
ho = 1.2
vo = 0.4
plot_width = width - ho
plot_height = height - vo
diffs = {}
ymin = numpy.inf
ymax = -numpy.inf
for n in ['Phillips', 'Nora']:
for meth in meth_names.keys():
cname = "%s_%s" % (meth, n)
diff = corr2[cname] - corr1[cname]
ymin = min(ymin, diff)
ymax = max(ymax, diff)
for meth in meth_names.keys():
cname = "%s_%s" % (meth, name)
diffs[meth] = corr2[cname] - corr1[cname]
yspan = ymax - ymin
ymin -= yspan * 0.05
ymax += yspan * 0.05
yspan = ymax - ymin
c = canvas.canvas()
g = graph.graphxy(width=plot_width, height=plot_height,
x=graph.axis.bar(painter=graph.axis.painter.bar(nameattrs=None)),
y=graph.axis.lin(painter=painter, min=ymin, max=ymax),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(parter=None, min=0, max=1))
w = plot_width / float(len(meth_names) + 1)
y0 = -ymin / yspan * plot_height
for i, meth in enumerate(methods):
col = method_colors[meth]
g.stroke( path.rect((i + 0.5) * w, y0, w, diffs[meth] / yspan * plot_height), [deco.filled([col])])
g.stroke( path.line(0, y0, plot_width, y0), [style.linestyle.dotted, style.linewidth.THin])
c.insert(g, [trafo.translate(ho, vo)])
c.text(0, plot_height * 0.5 + vo, r"$r_{0K} - r_{50K}$",
[text.halign.center, text.valign.top, text.size(-3), trafo.rotate(90)])
c.text(plot_width * 0.5 + ho, vo * 0.5, name,
[text.halign.center, text.valign.middle, text.size(-3)])
return c
def pyx_plotter(self):
from pyx import canvas, path, color
st = Stats(self.points)
if self.plot_range == AUTO:
xmax, xmin, ymax, ymin = st.bbox_auto(self.points)
else:
xmax, xmin, ymax, ymin = st.bbox()
wd, ht = xmax - xmin, ymax - ymin
sx = self.default_width / wd
sy = self.aspect_ratio * self.default_width / ht
#print 'WD:', wd, 'HT:', ht, sx, sy
clip = canvas.clip(path.rect(sx * xmin, sy * ymin, sx * wd, sy * ht))
c = canvas.canvas([clip])
#c.stroke(path.rect(sx*xmin, sy*ymin, sx*wd, sy*ht))
pth = path.path()
first_point = True
for p in self.points:
if first_point:
pth.append(path.moveto(sx * p.x, sy * p.y))
first_point = False
else:
pth.append(path.lineto(sx * p.x, sy * p.y))
c.stroke(pth)
for p in self.points:
if st.is_extreme_outlier(p):
c.fill(path.circle(sx * p.x, sy * p.y, 0.03), [color.rgb.red])
else:
c.fill(path.circle(sx * p.x, sy * p.y, 0.03))
return c
def acquisition_layer(holes):
# Get camera info
icenter = np.nonzero(
np.array(holes['holetype']) == b'ACQUISITION_CENTER')[0]
if (len(icenter) == 0):
return None
if (len(icenter) > 1):
print("Expect just one central acquisition camera.")
center_xfocal = np.array(holes['xfocal'])[icenter[0]]
center_yfocal = np.array(holes['yfocal'])[icenter[0]]
ioffaxis = np.nonzero(
np.array(holes['holetype']) == b'ACQUISITION_OFFAXIS')[0]
if (len(ioffaxis) == 0):
print("If there is a center acquisition camera we expect an off-axis.")
sys.exit()
if (len(ioffaxis) > 1):
print("Expect just one off-axis acquisition camera.")
sys.exit()
offaxis_xfocal = np.array(holes['xfocal'])[ioffaxis[0]]
offaxis_yfocal = np.array(holes['yfocal'])[ioffaxis[0]]
# Set up object to print
clippath = path.circle(0., 0., interior_radius)
clipobject = canvas.clip(clippath)
interior = canvas.canvas([clipobject])
interior.stroke(
path.circle(center_yfocal / 10., center_xfocal / 10., center_radius),
[style.linewidth.THick, color.cmyk.Black])
interior.stroke(
path.rect((offaxis_yfocal / 10.) - offaxis_ysize * 0.5,
(offaxis_xfocal / 10.) - offaxis_xsize * 0.5, offaxis_ysize,
offaxis_xsize), [style.linewidth.THick, color.cmyk.Black])
return interior
def pyx_plotter(self):
from pyx import canvas, path, color
st = Stats(self.points)
if self.plot_range == AUTO:
xmax, xmin, ymax, ymin = st.bbox_auto(self.points)
else:
xmax, xmin, ymax, ymin = st.bbox()
wd, ht = xmax - xmin, ymax - ymin
sx = self.default_width / wd
sy = self.aspect_ratio * self.default_width / ht
#print 'WD:', wd, 'HT:', ht, sx, sy
clip = canvas.clip(path.rect(sx * xmin, sy * ymin, sx * wd, sy * ht))
c = canvas.canvas([clip])
#c.stroke(path.rect(sx*xmin, sy*ymin, sx*wd, sy*ht))
pth = path.path()
first_point = True
for p in self.points:
if first_point:
pth.append(path.moveto(sx * p.x, sy * p.y))
first_point = False
else:
pth.append(path.lineto(sx * p.x, sy * p.y))
c.stroke(pth)
for p in self.points:
if st.is_extreme_outlier(p):
c.fill(path.circle(sx * p.x, sy * p.y, 0.03), [color.rgb.red])
else:
c.fill(path.circle(sx * p.x, sy * p.y, 0.03))
return c
def make_moon_key2_eng(canv, chart, y) :
x = 0.0
canv.fill(path.rect(x, y, chart.width, 1.0),
[color.rgb(0.0, 0.0, 0.0)])
for i in range(8) :
X = 1.0-(i+1.0)/9.0
canv.fill(waning_moon(X, 0.08, x+(i+4.0)/4.0, y+0.5),
[style.linejoin.bevel,mooncolorlight])
canv.text(x+1.8, y+0.7,
r'{\footnotesize\sffamily Waning Moon}',
[text.halign.center,text.valign.baseline,mooncolorlight])
canv.text(x+1.8, y+0.2,
r"{\scriptsize\sffamily (Moon rising)}",
[text.halign.center,text.valign.baseline,mooncolorlight])
for i in range(8) :
X = (i+1.0)/9.0
canv.fill(waxing_moon(X, 0.08, x+(i+4.0)/4.0+3.0, y+0.5),
[style.linejoin.bevel,mooncolordark])
canv.text(x+1.8+3.0, y+0.7,
r'{\footnotesize\sffamily Waxing Moon}',
[text.halign.center,text.valign.baseline,mooncolordark])
canv.text(x+1.8+3.0, y+0.2,
r"{\scriptsize\sffamily (Moon setting)}",
[text.halign.center,text.valign.baseline,mooncolordark])
# new moon, first quarter
# full moon, last quarter
canv.stroke(path.circle(x+8.5,y+0.75,.12),[mooncolorlight,pyx.deco.filled([mooncolordark])])
canv.text(x+8.25, y+0.65, r'{\footnotesize\sffamily New Moon}',
[text.halign.right,text.valign.baseline, mooncolordark])
canv.stroke(first_quarter_moon(0.12, x+8.9,y+0.75),[mooncolordark,pyx.deco.filled([mooncolordark])])
canv.text(x+9.25, y+0.65, r'{\footnotesize\sffamily First Quarter}',
[text.halign.left,text.valign.baseline, mooncolordark])
canv.stroke(path.circle(x+8.5,y+0.35,.12),[mooncolorlight,pyx.deco.filled([mooncolorlight])])
canv.text(x+8.25, y+0.25, r'{\footnotesize\sffamily Full Moon}',
[text.halign.right,text.valign.baseline, mooncolorlight])
canv.stroke(last_quarter_moon(0.12, x+8.9,y+0.35),[mooncolorlight,pyx.deco.filled([mooncolorlight])])
canv.text(x+9.25, y+0.25, r'{\footnotesize\sffamily Last Quarter}',
[text.halign.left,text.valign.baseline, mooncolorlight])
def make_moon_key2(canv, chart, y) :
x = 0.0
canv.fill(path.rect(x, y, chart.width-1.0, 1.0),
[color.rgb(0.0, 0.0, 0.0)])
for i in range(8) :
X = 1.0-(i+1.0)/9.0
canv.fill(waning_moon(X, 0.08, x+(i+4.0)/4.0, y+0.5),
[style.linejoin.bevel,mooncolorlight])
canv.text(x+1.8, y+0.7,
r'{\footnotesize\sffamily Küçülen Ay}',
[text.halign.center,text.valign.baseline,mooncolorlight])
canv.text(x+1.8, y+0.2,
r"{\scriptsize\sffamily (Ay'ın doğuş zamanları)}",
[text.halign.center,text.valign.baseline,mooncolorlight])
for i in range(8) :
X = (i+1.0)/9.0
canv.fill(waxing_moon(X, 0.08, x+(i+4.0)/4.0+3.0, y+0.5),
[style.linejoin.bevel,mooncolordark])
canv.text(x+1.8+3.0, y+0.7,
r'{\footnotesize\sffamily Büyüyen Ay}',
[text.halign.center,text.valign.baseline,mooncolordark])
canv.text(x+1.8+3.0, y+0.2,
r"{\scriptsize\sffamily (Ay'ın batış zamanları)}",
[text.halign.center,text.valign.baseline,mooncolordark])
# new moon, first quarter
# full moon, last quarter
canv.stroke(path.circle(x+8.5,y+0.7,.12),[mooncolorlight,pyx.deco.filled([mooncolordark])])
canv.text(x+8.25, y+0.6, r'{\footnotesize\sffamily Yeni Ay}',
[text.halign.right,text.valign.baseline, mooncolordark])
canv.stroke(first_quarter_moon(0.12, x+8.9,y+0.7),[mooncolordark,pyx.deco.filled([mooncolordark])])
canv.text(x+9.25, y+0.6, r'{\footnotesize\sffamily İlk Dördün}',
[text.halign.left,text.valign.baseline, mooncolordark])
canv.stroke(path.circle(x+8.5,y+0.3,.12),[mooncolorlight,pyx.deco.filled([mooncolorlight])])
canv.text(x+8.25, y+0.2, r'{\footnotesize\sffamily Dolunay}',
[text.halign.right,text.valign.baseline, mooncolorlight])
canv.stroke(last_quarter_moon(0.12, x+8.9,y+0.3),[mooncolorlight,pyx.deco.filled([mooncolorlight])])
canv.text(x+9.25, y+0.2, r'{\footnotesize\sffamily Son Dördün}',
[text.halign.left,text.valign.baseline, mooncolorlight])
def plot_bar(data, ranges, height, scale, split):
c = canvas.canvas()
pos = 0.0
x1 = 0.0
for i in range(5):
if str(i) in data:
x2 = data[str(i)] / 60.0 + pos
pos2 = x2
for j in range(1, ranges.shape[0]):
if x2 > ranges[j, 0] and x2 < ranges[j, 1]:
for k in range(j):
x2 -= ranges[k + 1, 0] - ranges[k, 1]
break
c.fill(path.rect(x1 * scale, 0, (x2 - x1) * scale, height),
[step_colors[i]])
split_pos = ranges[0, 1] * scale
for j in range(ranges.shape[0] - 1):
if pos2 > ranges[j, 1]:
c.insert(split, [trafo.translate(split_pos, height * 0.5)])
split_pos += (ranges[j + 1, 1] - ranges[j + 1, 0]) * scale
pos += data[str(i)] / 60.0
x1 = x2
return c
def rect(i0, j0, di=1, dj=1, txt=None):
extra = [green, style.linewidth.Thick, style.linestyle.dashed, trafo.translate(x, y)]
c.stroke(path.rect((i0-0.5)*dx, (j0-0.5)*dy, di*dx, dj*dy), extra)
if txt:
c.text((i0+di-0.5)*dx, (j0+dj-0.5)*dy-pip, txt,
[trafo.translate(x, y), text.halign.boxright, text.valign.top])
highlight = rgb(0.6, 0.6, 0.6)
#highlight = white
#highlight = rgb(1,1,0)
HH = 0.6*H
X0 = -10.
X1 = 0.
for X in [X0, X1]:
tr = trafo.translate(X, 0.)
for i in range(-3, 2):
extra = [highlight] if (i%2) else [shade]
c.fill(path.rect(2*i*r+r, 0, 2*r, HH), extra+[tr])
extra = [shade] if (i%2) else [highlight]
c.fill(path.rect(2*i*r+r, -HH, 2*r, HH), extra+[tr])
c.stroke(path.rect(-5*r, -HH, 10*r, 2*HH), [tr])
radius = 0.1
for x in [-3*r, -r, r, 3*r]:
c.fill(path.circle(x, 0., radius), [tr]) # focus
c.stroke(path.line(-8*r, 0, -6*r, 0), [deco.earrow()])
c.stroke(path.line(-8*r, -0.1, -8*r, +0.1))
c.text(-7*r, +0.2, r"$\sigma_i$", south)
c.text(X0-3*r, -0.4, "$...$", center)
c.text(X0-r, -0.4, "$i$", center)
y -= 3*dr
from pyx import metapost
from pyx.metapost.path import beginknot, endknot, smoothknot, tensioncurve
x0, y0 = tx0, ty0 = x, y
dx, dy = 1.5, 1.5
# Grid
for i in range(3):
c.stroke(path.line(x0+0.5*dx, y0-(i+1.0)*dy, x0+3.5*dx, y0-(i+1.0)*dy))
c.stroke(path.line(x0+(i+1.0)*dx, y0-0.5*dy, x0+(i+1.0)*dx, y0-3.5*dy))
c.stroke(path.rect(1.*dx + pip, -2.*dy + pip, dx-2*pip, dy-2*pip),
[green, style.linewidth.Thick, style.linestyle.dashed,
trafo.translate(tx0, ty0)])
def pair((x0, y0), (x1, y1), clr=None):
extra = [clr or blue, style.linewidth.Thick, style.linecap.round, trafo.translate(tx0, ty0)]
c.stroke(path.line(x0, y0, x1, y1), extra)
c.stroke(path.circle(x0, y0, 1.3*pip), extra)
c.stroke(path.circle(x1, y1, 1.3*pip), extra)
points0 = [
(1.3*dx, -1.7*dy), (1.3*dx, -2.5*dy),
(2.6*dx, -1.4*dy), (3.4*dx, -1.4*dy),
(1.7*dx, -1.7*dy), (1.7*dx, -2.5*dy)]
def draw_square(x, y, kante):
c.fill(path.rect(x, y, kante, kante), [color.grey(1)])
c.stroke(path.line(x, y, x + kante, y + kante),
[style.linewidth.thick, color.grey(0.5)])
c.stroke(path.rect(x, y, kante, kante), [style.linewidth.thick])
def main():
out_fname = sys.argv[1]
basedir = '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-2])
hic_phillips_fname1 = "%s/Data/HiC/HiCPipe/HM/mm9_ESC_NcoI_Phillips.hch" % basedir
hic_phillips_fname2 = "%s/Data/HiC/HiCPipe/HM/mm9_ESC_HindIII_Phillips.hch" % basedir
hic_nora_fname1 = "%s/Data/HiC/HiCPipe/HM/mm9_ESC_NcoI_Nora.hch" % basedir
hic_nora_fname2 = "%s/Data/HiC/HiCPipe/HM/mm9_ESC_HindIII_Nora.hch" % basedir
hic_phillips1 = h5py.File(hic_phillips_fname1, 'r')
hic_phillips2 = h5py.File(hic_phillips_fname2, 'r')
hic_nora1 = h5py.File(hic_nora_fname1, 'r')
hic_nora2 = h5py.File(hic_nora_fname2, 'r')
hm_phillips = {}
hm_nora = {}
for key in hic_phillips1.keys():
if key.count('unbinned_counts') == 0:
continue
region = int(key.split('.')[0])
hm_phillips[region] = dynamically_bin(hic_phillips1, hic_phillips2, region)
for key in hic_nora1.keys():
if key.count('unbinned_counts') == 0:
continue
region = int(key.split('.')[0])
hm_nora[region] = dynamically_bin(hic_nora1, hic_nora2, region)
fivec_fnames = {
"Prob_Phillips":"%s/Data/FiveC/HiFive/Phillips_ESC_probnodist.fcp" % basedir,
"Prob_Nora":"%s/Data/FiveC/HiFive/Nora_ESC_male_E14_probnodist.fcp" % basedir,
"Bin_Phillips":"%s/Data/FiveC/HiFive/Phillips_ESC_binnodist.fcp" % basedir,
"Bin_Nora":"%s/Data/FiveC/HiFive/Nora_ESC_male_E14_binnodist.fcp" % basedir,
"Exp_Phillips":"%s/Data/FiveC/HiFive/Phillips_ESC_expnodist.fcp" % basedir,
"Exp_Nora":"%s/Data/FiveC/HiFive/Nora_ESC_male_E14_expnodist.fcp" % basedir,
"Exp-KR_Phillips":"%s/Data/FiveC/HiFive/Phillips_ESC_expKRnodist.fcp" % basedir,
"Exp-KR_Nora":"%s/Data/FiveC/HiFive/Nora_ESC_male_E14_expKRnodist.fcp" % basedir,
}
data = {}
imgs = {}
ratio1 = 0
ratio2 = 0
for meth in ['Prob', 'Bin', 'Exp', 'Exp-KR']:
fc = hifive.FiveC(fivec_fnames["%s_Phillips" % meth])
fragments = fc.frags['fragments'][...]
regions = fc.frags['regions'][...]
counts = numpy.zeros(0, dtype=numpy.float64)
expected = numpy.zeros(0, dtype=numpy.float64)
hic_counts = numpy.zeros(0, dtype=numpy.float64)
hic_expected = numpy.zeros(0, dtype=numpy.float64)
skipped = []
for i in range(fc.frags['regions'].shape[0]):
temp = fc.cis_heatmap(i, datatype='fragment', arraytype='compact', binsize=0, skipfiltered=True)
if temp is None:
skipped.append(i)
continue
counts = numpy.hstack((counts, temp[:, :, 0].ravel()))
expected = numpy.hstack((expected, temp[:, :, 1].ravel()))
if i == 6:
ratio1 = temp.shape[1] / float(temp.shape[0])
imgs["%s_Phillips" % meth] = hifive.plotting.plot_full_array(temp, symmetricscaling=False)
if meth == 'Prob':
temp1 = numpy.zeros((temp.shape[0], temp.shape[1]), dtype=numpy.float32)
temp1[numpy.where(temp[:, :, 0] > 0.0)] = 1
if i == 6:
imgs["Raw_Phillips"] = hifive.plotting.plot_full_array(
numpy.dstack((temp[:, :, 0], temp1)), symmetricscaling=False)
binbounds = numpy.hstack((
fragments['start'][regions['start_frag'][i]:regions['stop_frag'][i]].reshape(-1, 1),
fragments['stop'][regions['start_frag'][i]:regions['stop_frag'][i]].reshape(-1, 1)))
valid = numpy.where(fc.filter[regions['start_frag'][i]:regions['stop_frag'][i]])[0]
binbounds = binbounds[valid, :]
temp = hm_phillips[i]
strands = fragments['strand'][regions['start_frag'][i]:regions['stop_frag'][i]][valid]
temp = temp[numpy.where(strands == 0)[0], :, :][:, numpy.where(strands == 1)[0], :]
hic_counts = numpy.hstack((hic_counts, temp[:, :, 0].ravel()))
hic_expected = numpy.hstack((hic_expected, temp[:, :, 1].ravel()))
if i == 6:
imgs["HiC_Phillips"] = hifive.plotting.plot_full_array(temp, symmetricscaling=False)
if meth == 'Prob':
data["Raw_Phillips"] = numpy.copy(counts)
where = numpy.where(hic_expected > 0.0)[0]
hic_counts[where] /= hic_expected[where]
data["HiC_Phillips"] = numpy.copy(hic_counts)
where = numpy.where(expected > 0.0)[0]
counts[where] /= expected[where]
data["%s_Phillips" % meth] = numpy.copy(counts)
fc = hifive.FiveC(fivec_fnames["%s_Nora" % meth])
temp = fc.cis_heatmap(0, datatype='fragment', arraytype='compact', binsize=0, skipfiltered=True)
ratio2 = temp.shape[1] / float(temp.shape[0])
imgs["%s_Nora" % meth] = hifive.plotting.plot_full_array(temp, symmetricscaling=False)
counts = temp[:, :, 0].ravel()
expected = temp[:, :, 1].ravel()
if meth == 'Prob':
temp1 = numpy.zeros((temp.shape[0], temp.shape[1]), dtype=numpy.float32)
temp1[numpy.where(temp[:, :, 0] > 0.0)] = 1
imgs["Raw_Nora"] = hifive.plotting.plot_full_array(
numpy.dstack((temp[:, :, 0], temp1)), symmetricscaling=False)
data["Raw_Nora"] = numpy.copy(counts)
fragments = fc.frags['fragments'][...]
regions = fc.frags['regions'][...]
binbounds = numpy.hstack((
fragments['start'][regions['start_frag'][0]:regions['stop_frag'][0]].reshape(-1, 1),
fragments['stop'][regions['start_frag'][0]:regions['stop_frag'][0]].reshape(-1, 1)))
binbounds = binbounds[numpy.where(fc.filter[regions['start_frag'][0]:regions['stop_frag'][0]])[0], :]
temp = hm_nora[0]
strands = fragments['strand'][regions['start_frag'][0]:regions['stop_frag'][0]]
temp = temp[numpy.where(strands==0)[0], :, :][:, numpy.where(strands == 1)[0], :]
imgs["HiC_Nora"] = hifive.plotting.plot_full_array(temp, symmetricscaling=False)
hic_counts = temp[:, :, 0].ravel()
hic_expected = temp[:, :, 1].ravel()
where = numpy.where(hic_expected > 0.0)[0]
hic_counts[where] /= hic_expected[where]
data["HiC_Nora"] = numpy.copy(hic_counts)
where = numpy.where(expected > 0.0)[0]
counts[where] /= expected[where]
data["%s_Nora" % meth] = numpy.copy(counts)
correlations = {}
output = open(out_fname.replace('pdf', 'txt'), 'w')
print >> output, "Method\tPhillips\tNora"
for meth in methods:
temp = [meth]
for name in ["Phillips", "Nora"]:
valid = numpy.where((data["%s_%s" % (meth, name)] > 0.0) * (data["HiC_%s" % name] > 0.0))
correlations["%s_%s" % (meth, name)] = numpy.corrcoef(numpy.log(data["%s_%s" % (meth, name)][valid]),
numpy.log(data["HiC_%s" % name][valid]))[0, 1]
temp.append(str(correlations["%s_%s" % (meth, name)]))
print >> output, '\t'.join(temp)
output.close()
width = 16.8
spacer = 0.3
c = canvas.canvas()
plot_width = (width - spacer * 3.0 - 0.4) / 4.0
for i, meth in enumerate(["Raw", "Prob", "HiC"]):
meth_names = {"Raw":"Raw", "Prob":"HiFive", "HiC":"HiC"}
c.text(plot_width * (i + 1.5) + spacer * (i + 1), (ratio1 + ratio2) * plot_width + spacer + 0.1,
"%s" % meth_names[meth], [text.halign.center, text.valign.bottom, text.size(-2)])
c.insert(bitmap.bitmap(0, 0, imgs["%s_Phillips" % meth], width=plot_width),
[trafo.translate((i + 1) * (plot_width + spacer), plot_width * ratio2 + spacer)])
c.insert(bitmap.bitmap(0, 0, imgs["%s_Nora" % meth], width=plot_width),
[trafo.translate((i + 1) * (plot_width + spacer), 0)])
g = graph.graphxy(width=plot_width - 0.8, height=plot_width * ratio1,
x=graph.axis.nestedbar(painter=graph.axis.painter.bar(nameattrs=None)),
y=graph.axis.lin(painter=painter),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(parter=None, min=0, max=1))
for i, meth in enumerate(methods):
Y = numpy.zeros(2, dtype=numpy.float32)
col = method_colors[meth]
for j, name in enumerate(["Phillips", "Nora"]):
Y[j] = correlations["%s_%s" % (meth, name)]
g.plot(graph.data.points(zip(zip(range(Y.shape[0]), [i] * Y.shape[0]), Y), xname=1, y=2),
[graph.style.changebar([col])])
g.text(-0.8, plot_width * ratio1 * 0.5, "Correlation",
[text.halign.center, text.valign.top, text.size(-3), trafo.rotate(90)])
g.text((plot_width - 0.8) * 0.25, -0.1, "Phillips",
[text.halign.center, text.valign.top, text.size(-3)])
g.text((plot_width - 0.8) * 0.75, -0.1, "Nora",
[text.halign.center, text.valign.top, text.size(-3)])
c.insert(g, [trafo.translate(0.8, plot_width * ratio2 + spacer)])
c.text(width, (ratio1 + ratio2 * 0.5) * plot_width + spacer, "Phillips",
[text.halign.center, text.valign.top, trafo.rotate(-90), text.size(-2)])
c.text(width, ratio1 * 0.5 * plot_width, "Nora",
[text.halign.center, text.valign.top, trafo.rotate(-90), text.size(-2)])
meth_names = {"Raw":"Raw", "Prob":"HiFive-Probability", "Exp":"HiFive-Express", "Bin":"HiFive-Binning",
"Exp-KR":"HiFive-ExpressKR", "Exp-KR-dist":"HiFive-ExpressKR-dist"}
for i, meth in enumerate(methods):
c.fill(path.rect(1.0, plot_width * ratio1 - 1.0 - i * 0.5, 0.2, 0.2), [method_colors[meth]])
c.text(1.3, plot_width * ratio1 - 0.9 - i * 0.5, "%s" % meth_names[meth],
[text.halign.left, text.valign.middle, text.size(-3)])
c.writePDFfile(out_fname)
from pyx import canvas, color, deco, path, text, trafo
text.set(text.LatexRunner)
c = canvas.canvas()
codepoint = 0x00E9
bits = 16
codepointbinary = [(codepoint & 2**n)/2**n for n in range(bits)]
codepointbinary.reverse()
size = 0.4
x0 = 0
y0 = 3
dy = 0.07
c.fill(path.rect(x0, y0, 5*size, size),
[color.grey(0.5), deco.stroked([color.grey(0.5)])])
c.stroke(path.rect(x0+5*size, y0, 5*size, size))
c.stroke(path.rect(x0+10*size, y0, 6*size, size))
for n in range(len(codepointbinary)):
c.text(x0+(n+0.5)*size, y0+dy, r"\sffamily %i" % codepointbinary[n],
[text.halign.center])
p = path.path(path.moveto(0.2*size, size+0.03),
path.lineto(0.2*size, size+0.07),
path.lineto(3.8*size, size+0.07),
path.lineto(3.8*size, size+0.03))
for n in range(bits//4):
c.stroke(p, [trafo.translate(4*n*size, y0)])
c.text((4*n+2)*size, size+0.14+y0, r"\sffamily %X" %
(codepoint >> (bits//4-n-1)*4 & 0x0f),
x, y = 0., 0.
frame()
for i in range(3):
a = 0.1*i+0.3
c.stroke(path.line(x, y+a*h, x+w, y+(a+0.0)*h), st_tau)
dx = 0.2*w
for i in range(3, 6):
a = 0.1*i+0.3
c.stroke(path.line(x+0.18*w+dx, y+a*h, x+0.20*w+dx, y+(a+0.00)*h), st_tau)
c.fill(path.rect(x+0.2*w+dx, y, x+0.25*w+dx, y+h), [white])
c.text(x+0.2*w+dx, y+0.55*h, r"$\Big\} k$", west)
x += 1.1*w
c.text(x, y+0.5*h, r"$= f_{k-1}$", west)
x += 0.8*w
frame()
c.stroke(path.line(x, y+0.5*h, x+w, y+0.5*h), st_vac)
x += 1.1*w
c.text(x, y+0.5*h, r"$+ f_k$", west)
c = old_c
old_c = None
# --------------------------------------------------------------------
w, h = 1.0, 1.0
m = 0.1
#x0, y0 = 0.6, h + 10*m
x0, y0 = 0., 0.
push()
#c.text(x0-0.8, y0, "(a)")
c.stroke(path.rect(x0, y0, w, h), dashed)
c.stroke(path.rect(x0+w+m, y0, w, h), dotted)
grarrow = [green, style.linewidth.THick, deco.earrow(size=0.2)]
y = y0+0.3*h
c.stroke(path.line(x0+0.5*w, y, x0+1.5*w+m, y), grarrow)
anyon(x0+0.8*w, y)
anyon(x0+m+1.2*w, y)
y = y0+0.7*h
c.stroke(path.line(x0+1.5*w+m, y, x0+0.5*w, y), grarrow)
anyon(x0+0.8*w, y)
anyon(x0+m+1.2*w, y)
pop([trafo.rotate(-90), trafo.translate(0.7, 2.5*h)])
text.set(text.LatexRunner)
text.preamble(r'''\usepackage[T1]{fontenc}
\usepackage{bera}
\renewcommand*\familydefault{\ttdefault}
\usepackage{color}
\definecolor{ex1}{rgb}{0, 0, 0.7}
\definecolor{ex2}{rgb}{0, 0.6, 0}
\definecolor{ex3}{rgb}{0.7, 0, 0}''')
unit.set(xscale=1.2)
c = canvas.canvas()
ex1color = color.rgb(0, 0, 0.7)
linewidth = 0.1*boxsize
for n in (0, 2, 5):
c.fill(path.rect(n*boxsize+linewidth, linewidth,
boxsize-2*linewidth, 3*boxsize-2*linewidth),
[ex1color])
c.fill(path.rect(n*boxsize+2*linewidth, 2*linewidth,
boxsize-4*linewidth, 3*boxsize-4*linewidth),
[color.grey(1)])
ex2color = color.rgb(0, 0.6, 0)
linewidth = 0.1
for n in range(5):
markbox((n+1)*boxsize, (ncols-n-1)*boxsize, ex2color)
ex3color = color.rgb(0.7, 0, 0)
linewidth = 0.1
for n in (0, 2, 5):
markbox(2*boxsize, (ncols-n-1)*boxsize, ex3color)
