def svg():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
except:
session.flash = "no tree '%s'" % i
redirect("index")
opts = t.printopts
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
off = t.printopts.border
node.translate(off, off)
d = drawtree.draw(node, opts)
#d.scale(1.9,1.9)
x1, y1, x2, y2 = d.getBounds()
d.width = (x2 - x1) * 0.63
d.height = (y2 - y1) * 0.598
response.headers["Content-Type"] = "image/svg"
f = t.printopts.title + ".svg"
s = "attachment; filename=%s" % f
response.headers["Content-Disposition"] = s
return drawtree.render_svg(d, opts)
def pdf2svg():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
if request.vars.ladderize:
t.root.order_subtrees_by_size(recurse=True,
reverse=bool(request.vars.rev))
except:
session.flash = "no tree '%s'" % i
redirect("index")
fname = "tred-" + response.session_id
opts = t.printopts
v = request.vars
if v.parsevars:
t.labelfilter = v.labelfilter or ""
t.labeltype = v.labeltype or t.labeltype
t.labelsort = v.labelsort or t.labelsort
opts.title = v.title or opts.title or "%s-%s" % (t.source, t.name)
opts.pagesize = v.pagesize or opts.pagesize or "letter"
#print opts.pagesize
opts.draw_phylogram = v.draw_phylogram and t.phylogram
opts.baseheight = float(v.baseheight or 0) or opts.baseheight
opts.unitwidth = float(v.unitwidth or 0) or opts.unitwidth
opts.border = float(v.border or 0) or opts.border
opts.vpad = float(v.vpad or 1.1)
if v.draw_intlabels and "intlabel" not in opts.visible:
opts.visible.append("intlabel")
if (not v.draw_intlabels) and "intlabel" in opts.visible:
opts.visible.remove("intlabel")
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
d = drawtree.draw(node, opts)
t.drawing = d
buf = drawtree.render_pdf(d, opts)
proc = subprocess.Popen(("/usr/bin/pstoedit", "-f", "plot-svg"),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
out, err = proc.communicate(buf.getvalue())
out = out.split("\n")
out[2] = '<svg version="1.1" baseProfile="full" id="body" '\
'width="%s" height="%s" viewBox="0 0 1 1" '\
'preserveAspectRatio="none" '\
'xmlns="http://www.w3.org/2000/svg" '\
'xmlns:xlink="http://www.w3.org/1999/xlink" '\
'xmlns:ev="http://www.w3.org/2001/xml-events">' \
% (d.width, d.height)
out[5] = ""
response.headers["Content-Type"] = "image/svg"
f = t.printopts.title + ".svg"
s = "attachment; filename=%s" % f
response.headers["Content-Disposition"] = s
return "\n".join(out)
def svg():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
except:
session.flash = "no tree '%s'" % i
redirect("index")
opts = t.printopts
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
off = t.printopts.border
node.translate(off, off)
d = drawtree.draw(node, opts)
# d.scale(1.9,1.9)
x1, y1, x2, y2 = d.getBounds()
d.width = (x2 - x1) * 0.63
d.height = (y2 - y1) * 0.598
response.headers["Content-Type"] = "image/svg"
f = t.printopts.title + ".svg"
s = "attachment; filename=%s" % f
response.headers["Content-Disposition"] = s
return drawtree.render_svg(d, opts)
def pdf2svg():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
if request.vars.ladderize:
t.root.order_subtrees_by_size(recurse=True, reverse=bool(request.vars.rev))
except:
session.flash = "no tree '%s'" % i
redirect("index")
fname = "tred-" + response.session_id
opts = t.printopts
v = request.vars
if v.parsevars:
t.labelfilter = v.labelfilter or ""
t.labeltype = v.labeltype or t.labeltype
t.labelsort = v.labelsort or t.labelsort
opts.title = v.title or opts.title or "%s-%s" % (t.source, t.name)
opts.pagesize = v.pagesize or opts.pagesize or "letter"
# print opts.pagesize
opts.draw_phylogram = v.draw_phylogram and t.phylogram
opts.baseheight = float(v.baseheight or 0) or opts.baseheight
opts.unitwidth = float(v.unitwidth or 0) or opts.unitwidth
opts.border = float(v.border or 0) or opts.border
opts.vpad = float(v.vpad or 1.1)
if v.draw_intlabels and "intlabel" not in opts.visible:
opts.visible.append("intlabel")
if (not v.draw_intlabels) and "intlabel" in opts.visible:
opts.visible.remove("intlabel")
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
d = drawtree.draw(node, opts)
t.drawing = d
buf = drawtree.render_pdf(d, opts)
proc = subprocess.Popen(("/usr/bin/pstoedit", "-f", "plot-svg"), stdin=subprocess.PIPE, stdout=subprocess.PIPE)
out, err = proc.communicate(buf.getvalue())
out = out.split("\n")
out[2] = (
'<svg version="1.1" baseProfile="full" id="body" '
'width="%s" height="%s" viewBox="0 0 1 1" '
'preserveAspectRatio="none" '
'xmlns="http://www.w3.org/2000/svg" '
'xmlns:xlink="http://www.w3.org/1999/xlink" '
'xmlns:ev="http://www.w3.org/2001/xml-events">' % (d.width, d.height)
)
out[5] = ""
response.headers["Content-Type"] = "image/svg"
f = t.printopts.title + ".svg"
s = "attachment; filename=%s" % f
response.headers["Content-Disposition"] = s
return "\n".join(out)
def pdfsingle():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
if request.vars.ladderize:
t.root.order_subtrees_by_size(recurse=True,
reverse=bool(request.vars.rev))
except:
session.flash = "no tree '%s'" % i
redirect("index")
fname = "tred-" + response.session_id
opts = t.printopts
v = request.vars
if v.parsevars:
t.labelfilter = v.labelfilter or ""
t.labeltype = v.labeltype or t.labeltype
t.labelsort = v.labelsort or t.labelsort
opts.title = v.title or opts.title or "%s-%s" % (t.source, t.name)
opts.pagesize = v.pagesize or opts.pagesize or "letter"
#print opts.pagesize
opts.draw_phylogram = v.draw_phylogram and t.phylogram
opts.baseheight = float(v.baseheight or 0) or opts.baseheight
opts.unitwidth = float(v.unitwidth or 0) or opts.unitwidth
opts.border = float(v.border or 0) or opts.border
opts.vpad = float(v.vpad or 1.1)
if v.draw_intlabels and "intlabel" not in opts.visible:
opts.visible.append("intlabel")
if (not v.draw_intlabels) and "intlabel" in opts.visible:
opts.visible.remove("intlabel")
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
d = drawtree.draw(node, opts)
t.drawing = d
buf = drawtree.render_pdf(d, opts)
response.headers["Content-Type"] = "application/x-pdf"
f = t.printopts.title + ".pdf"
s = "attachment; filename=%s" % f
response.headers["Content-Disposition"] = s
return buf.getvalue()
def pdfsingle():
tlist = get_treelist()
try:
i = int(request.vars.i)
t = tlist.trees[i]
if request.vars.ladderize:
t.root.order_subtrees_by_size(recurse=True, reverse=bool(request.vars.rev))
except:
session.flash = "no tree '%s'" % i
redirect("index")
fname = "tred-" + response.session_id
opts = t.printopts
v = request.vars
if v.parsevars:
t.labelfilter = v.labelfilter or ""
t.labeltype = v.labeltype or t.labeltype
t.labelsort = v.labelsort or t.labelsort
opts.title = v.title or opts.title or "%s-%s" % (t.source, t.name)
opts.pagesize = v.pagesize or opts.pagesize or "letter"
# print opts.pagesize
opts.draw_phylogram = v.draw_phylogram and t.phylogram
opts.baseheight = float(v.baseheight or 0) or opts.baseheight
opts.unitwidth = float(v.unitwidth or 0) or opts.unitwidth
opts.border = float(v.border or 0) or opts.border
opts.vpad = float(v.vpad or 1.1)
if v.draw_intlabels and "intlabel" not in opts.visible:
opts.visible.append("intlabel")
if (not v.draw_intlabels) and "intlabel" in opts.visible:
opts.visible.remove("intlabel")
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
d = drawtree.draw(node, opts)
t.drawing = d
buf = drawtree.render_pdf(d, opts)
response.headers["Content-Type"] = "application/x-pdf"
f = t.printopts.title + ".pdf"
s = "attachment; filename=%s" % f
response.headers["Content-Disposition"] = s
return buf.getvalue()
def printer():
tlist = get_treelist()
try:
i = int(request.vars.i)
except TypeError:
redirect("index")
try:
t = tlist.trees[i]
except IndexError:
session.flash = "no tree '%s'" % i
redirect("index")
if request.vars.ladderize:
t.root.order_subtrees_by_size(recurse=True,
reverse=bool(request.vars.rev))
t.newick = newick.tostring(t.root) + ";"
fname = "tred-" + response.session_id
opts = t.printopts
v = request.vars
if v.parsevars:
t.labelfilter = v.labelfilter or ""
t.labeltype = v.labeltype or t.labeltype
t.labelsort = v.labelsort or t.labelsort
opts.title = v.title or opts.title or "%s-%s" % (t.source, t.name)
opts.pagesize = v.pagesize or opts.pagesize or "letter"
#print opts.pagesize
opts.draw_phylogram = v.draw_phylogram and t.phylogram
opts.baseheight = float(v.baseheight or 0) or opts.baseheight
opts.unitwidth = float(v.unitwidth or 0) or opts.unitwidth
opts.border = float(v.border or 0) or opts.border
opts.vpad = float(v.vpad or 1.1)
if v.draw_intlabels and "intlabel" not in opts.visible:
opts.visible.append("intlabel")
if (not v.draw_intlabels) and "intlabel" in opts.visible:
opts.visible.remove("intlabel")
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
d = drawtree.draw(node, opts)
t.drawing = d
buf = StringIO()
npages, scalefact = drawtree.render_multipage(d, opts, buf)
f = open("/tmp/%s.pdf" % fname, "w")
f.write(buf.getvalue())
f.close()
# use graphicsmagick convert (page numbers *.png.0, *.png.1, ...)
commands.getoutput("rm /tmp/%s*.png*" % fname)
cmd = "convert /tmp/%s.pdf /tmp/%s.png" % (fname, fname)
exit, out = commands.getstatusoutput(cmd)
# pngs = glob.glob("/tmp/%s*.png*" % fname)
if npages > 1:
pngs = ['%s.png.%s' % (fname, i) for i in range(npages)]
else:
pngs = ['%s.png' % fname]
if scalefact < 1.0:
response.flash = "To fit the page width, "\
"the drawing has been scaled by %0.2f" % scalefact
return dict(tree=t, pngs=pngs)
def printer():
tlist = get_treelist()
try:
i = int(request.vars.i)
except TypeError:
redirect("index")
try:
t = tlist.trees[i]
except IndexError:
session.flash = "no tree '%s'" % i
redirect("index")
if request.vars.ladderize:
t.root.order_subtrees_by_size(recurse=True, reverse=bool(request.vars.rev))
t.newick = newick.tostring(t.root) + ";"
fname = "tred-" + response.session_id
opts = t.printopts
v = request.vars
if v.parsevars:
t.labelfilter = v.labelfilter or ""
t.labeltype = v.labeltype or t.labeltype
t.labelsort = v.labelsort or t.labelsort
opts.title = v.title or opts.title or "%s-%s" % (t.source, t.name)
opts.pagesize = v.pagesize or opts.pagesize or "letter"
# print opts.pagesize
opts.draw_phylogram = v.draw_phylogram and t.phylogram
opts.baseheight = float(v.baseheight or 0) or opts.baseheight
opts.unitwidth = float(v.unitwidth or 0) or opts.unitwidth
opts.border = float(v.border or 0) or opts.border
opts.vpad = float(v.vpad or 1.1)
if v.draw_intlabels and "intlabel" not in opts.visible:
opts.visible.append("intlabel")
if (not v.draw_intlabels) and "intlabel" in opts.visible:
opts.visible.remove("intlabel")
node, mapping = drawtree.traverse(t.root, opts)
thicken_branches(node)
node.set_attr("vpad", opts.vpad, 1)
d = drawtree.draw(node, opts)
t.drawing = d
buf = StringIO()
npages, scalefact = drawtree.render_multipage(d, opts, buf)
f = open("/tmp/%s.pdf" % fname, "w")
f.write(buf.getvalue())
f.close()
# use graphicsmagick convert (page numbers *.png.0, *.png.1, ...)
commands.getoutput("rm /tmp/%s*.png*" % fname)
cmd = "convert /tmp/%s.pdf /tmp/%s.png" % (fname, fname)
exit, out = commands.getstatusoutput(cmd)
# pngs = glob.glob("/tmp/%s*.png*" % fname)
if npages > 1:
pngs = ["%s.png.%s" % (fname, i) for i in range(npages)]
else:
pngs = ["%s.png" % fname]
if scalefact < 1.0:
response.flash = "To fit the page width, " "the drawing has been scaled by %0.2f" % scalefact
return dict(tree=t, pngs=pngs)